python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.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 2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.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 2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-cln3-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-cln3-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-whi5-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-whi5-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-H3.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-Input.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.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 2017-12-27-WT-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2017-12-27-WT-Pol2.sacCer3+Schizosaccharomyces_pombe.a.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 2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.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 2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-cln3-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-cln3-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-Input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-cln3-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-cln3-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-cln3-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-cln3-Pol2.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-whi5-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-whi5-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-Input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-whi5-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-whi5-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-whi5-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-whi5-Pol2.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-WT-H3.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-WT-Input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-Input.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-WT-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-Pol2pS2.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-WT-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-Pol2pS5.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2017-12-27-WT-Pol2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2017-12-27-WT-Pol2.sacCer3+Schizosaccharomyces_pombe.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-A-YPD-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-B-YPD-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-C-SCE_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-D-SCE-Pol2pS2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-E-SCE-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-F-SCE-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-G-YPD-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-H-SCD_noAA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-I-SCD_Rpb1_AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-J-SCD_TBP-AA-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-K-SCD_noAA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-L-SCD_Rpb1_AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-M-SCD_TBP-AA-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-N-YPD-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-O-SCE-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-P-SCD_noAA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-Q-SCD_Rpb1_AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-R-SCD_TBP-AA-CTD.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-S-SCD_noAA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-T-YPD-Pol2pS5_C.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-U-YPD-Pol2pS5_D.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-V-YPD-Pol2pS5_E.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-W-SCD_Rpb1_AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-02-13-X-SCD_TBP-AA-Rpb3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-H3-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Input-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS5-L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS5-L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS5-L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2pS5-L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_0.0625.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_0.25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_0.5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-04-20-Pol2-SC_ratio_4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-H3-180529_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-Input-180529_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-Pol2-180529_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-RNAPII_pS2-180529_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-0nM-RNAPII_pS5-180529_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-H3-180529_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-Input-180529_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-Pol2-180529_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-RNAPII_pS2-180529_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-10nM-RNAPII_pS5-180529_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-H3-180529_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-Input-180529_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-Pol2-180529_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-RNAPII_pS2-180529_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS63-30nM-RNAPII_pS5-180529_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-H3-180525_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-Input-180525_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-Pol2-180525_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-RNAPII_pS2-180525_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS80-RNAPII_pS5-180525_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-H3-180525_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-Input-180525_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-Pol2-180525_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-RNAPII_pS2-180525_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-MS81-RNAPII_pS5-180525_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-H3-180522_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-Input-180522_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_0min_+rap-Pol2-180522_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-H3-180522_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-Input-180522_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_10min_+rap-Pol2-180522_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-H3-180522_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-Input-180522_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_20min_+rap-Pol2-180522_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-H3-180522_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-Input-180522_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_30min_+rap-Pol2-180522_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-H3-180522_L25.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-Input-180522_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-RNAPII_AA_60min_+rap-Pol2-180522_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_0min_+rap-H3-180522_L26.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_0min_+rap-Input-180522_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_0min_+rap-Pol2-180522_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_10min_+rap-H3-180522_L27.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_10min_+rap-Input-180522_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_10min_+rap-Pol2-180522_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_20min_+rap-H3-180522_L28.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_20min_+rap-Input-180522_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_20min_+rap-Pol2-180522_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_30min_+rap-H3-180522_L29.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_30min_+rap-Input-180522_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_30min_+rap-Pol2-180522_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_60min_+rap-H3-180522_L30.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_60min_+rap-Input-180522_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-TBP_AA_60min_+rap-Pol2-180522_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-H3-180525_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-H3-180531_L19.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-Input-180525_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-Input-180531_L1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-Pol2-180525_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-Pol2-180531_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS2-180525_L7.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS2-180531_L13.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.1-RNAPII_pS5-180525_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.2-H3-180531_L20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.2-Input-180531_L2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.2-Pol2-180531_L8.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.2-RNAPII_pS2-180531_L14.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.3-H3-180531_L21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.3-Input-180531_L3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.3-Pol2-180531_L9.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.3-RNAPII_pS2-180531_L15.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.4-H3-180531_L22.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.4-Input-180531_L4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.4-Pol2-180531_L10.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.4-RNAPII_pS2-180531_L16.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.5-H3-180531_L23.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.5-Input-180531_L5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.5-Pol2-180531_L11.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.5-RNAPII_pS2-180531_L17.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.6-H3-180531_L24.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.6-Input-180531_L6.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.6-Pol2-180531_L12.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-06-16-WT_OD_0.6-RNAPII_pS2-180531_L18.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_15-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_15-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_15-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_5-H3-rep1-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_5-H3-rep2-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS80_5-input-whi5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_15-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_15-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_15-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_5-H3-rep1-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_5-H3-rep2-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-07-12-MS81_5-input-cln3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L10-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L11-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L12-MS81-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L13-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L14-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L15-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L16-MS63-0nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L17-MS63-0nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L18-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L19-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L20-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L21-MS63-10nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L22-MS63-10nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L23-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L24-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L25-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L26-MS63-30nM-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L27-MS63-30nM-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L28-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L29-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L2-MS1-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L30-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L3-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L4-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L5-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L6-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L7-MS80-input-2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L8-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180718-L9-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L10-MS63-10nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L11-MS63-10nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L12-MS63-10nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L13-MS63-30nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L14-MS63-30nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L15-MS63-30nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L16-MS63-30nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L17-MS63-30nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L18-MS63-30nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L1-MS63-0nM-input1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L2-MS63-0nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L3-MS63-0nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L4-MS63-0nM-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L5-MS63-0nM-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L6-MS63-0nM-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L7-MS63-10nM-input2.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L8-MS63-10nM-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180723-L9-MS63-10nM-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L10-MS80-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L11-MS80-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L12-MS80-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L13-MS81-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L14-MS81-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L15-MS81-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L16-MS81-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L17-MS81-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L18-MS81-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L19-MS55-1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L1-MS1-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L20-MS55-1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L21-MS55-1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L22-MS55-1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L23-MS55-1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L24-MS55-1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L25-MS55-2-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L26-MS55-2-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L27-MS55-2-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L28-MS55-2-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L29-MS55-2-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L2-MS1-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L30-MS55-2-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L31-MS55-3-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L32-MS55-3-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L33-MS55-3-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L34-MS55-3-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L35-MS55-3-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L36-MS55-3-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L37-MS55-4-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L38-MS55-4-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L39-MS55-4-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L3-MS1-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L40-MS55-4-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L41-MS55-4-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L42-MS55-4-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L4-MS1-AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L5-MS1-AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L6-MS1-AB21.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L7-MS80-input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L8-MS80-AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-09-13-180731-L9-MS80-AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s10-2-180917_L10_MS231_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s1-1-180917_L01_MS230_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s11-3-180917_L11_MS232_DMSO_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s12-3-180917_L12_MS232_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s13-3-180917_L13_MS232_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s14-3-180917_L14_MS232_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s15-3-180917_L15_MS232_DMSO_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s16-4-180917_L16_MS230_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s17-4-180917_L17_MS230_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s18-4-180917_L18_MS230_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s19-4-180917_L19_MS230_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s20-4-180917_L20_MS230_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s2-1-180917_L02_MS230_DMSO_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s21-5-180917_L21_MS231_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s22-5-180917_L22_MS231_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s23-5-180917_L23_MS231_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s24-5-180917_L24_MS231_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s25-5-180917_L25_MS231_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s26-6-180917_L26_MS232_RAPA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s27-6-180917_L27_MS232_RAPA_AB1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s28-6-180917_L28_MS232_RAPA_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s29-6-180917_L29_MS232_RAPA_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s30-6-180917_L30_MS232_RAPA_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s3-1-180917_L03_MS230_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s76-23-180821_L01_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s77-23-180821_L02_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s78-23-180821_L03_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s79-23-180821_L04_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s80-23-180821_L05_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s81-23-180821_L06_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s8-2-180917_L8_MS231_DMSO_AB4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s82-23-180821_L07_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s83-23-180821_L08_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s84-23-180821_L09_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s85-23-180821_L10_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s86-24-180827_L1_MS1_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s87-24-180827_L2_MS1_AB20.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s88-24-180827_L3_MS1_AB39.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s89-24-180827_L4_MS1_AB41.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s90-24-180827_L5_MS1_AB42.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s91-24-180827_L6_MS1_AB43.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s9-2-180917_L9_MS231_DMSO_AB5.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s92-24-180827_L7_MS1_AB44.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s93-24-180827_L8_MS1_AB45.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s94-24-180827_L9_MS1_AB46.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s95-24-180827_L10_MS1_AB47.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2018-10-14-s96-24-180827_L11_MS1_AB48.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L01_MS1_input-S01_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L02_MS80_input-S02_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L03_MS81_input-S03_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L04_MS63_0nM_input-S04_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L05_MS63_10nM_input-S05_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L06_MS63_30nM_input-S06_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L07_MS1_AB20-S07_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L08_MS80_AB20-S08_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L09_MS81_AB20-S09_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L13_MS1_AB21-S13_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L14_MS80_AB21-S14_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L15_MS81_AB21-S15_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L19_MS1_AB39-S19_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L20_MS80_AB39-S20_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L21_MS81_AB39-S21_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L25_MS1_AB41-S25_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L26_MS80_AB41-S26_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L27_MS81_AB41-S27_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L31_MS1_AB42-S31_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L32_MS80_AB42-S32_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L33_MS81_AB42-S33_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L37_MS1_AB43-S37_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L38_MS80_AB43-S38_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L39_MS81_AB43-S39_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L43_MS1_AB44-S43_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L44_MS80_AB44-S44_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L45_MS81_AB44-S45_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L49_MS1_AB45-S49_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L50_MS80_AB45-S50_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L51_MS81_AB45-S51_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L55_MS1_AB46-S55_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L56_MS80_AB46-S56_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L57_MS81_AB46-S57_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L61_MS1_AB47-S61_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L62_MS80_AB47-S62_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L63_MS81_AB47-S63_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L67_MS1_AB48-S67_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L68_MS80_AB48-S68_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L69_MS81_AB48-S69_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM