python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/181030L01-S18_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L01-S18_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/181030L02-S19_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L02-S19_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/181030L03-S20_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L03-S20_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/181030L04-S21_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L04-S21_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/181030L05-S22_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L05-S22_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/181030L06-S23_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L06-S23_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/181030L07-S24_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L07-S24_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/181030L08-S25_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L08-S25_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/181030L09-S26_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L09-S26_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/181030L10-S27_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L10-S27_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/181030L11-S28_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L11-S28_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/181030L12-S29_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L12-S29_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/181030L13-S30_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L13-S30_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/181030L14-S31_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L14-S31_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/181030L15-S32_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L15-S32_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/181030L16-S33_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L16-S33_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/181030L17-S34_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L17-S34_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/181030L18-S35_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L18-S35_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/181030L19-S36_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L19-S36_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/181126L01_MS405_sp114_mix1_input-S01_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/181126L02_MS405_sp114_mix2_input-S02_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/181126L03_MS407_sp116_mix1_input-S03_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/181126L04_MS407_sp116_mix2_input-S04_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/181126L05_MS1_sp108_input-S05_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L05_MS1_sp108_input-S05_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/181126L06_MS407_sp108_input-S06_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L06_MS407_sp108_input-S06_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/181126L07_MS405_sp114_mix1_ab102A-S07_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/181126L08_MS405_sp114_mix1_ab102B-S08_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/181126L09_MS405_sp114_mix2_ab102A-S09_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/181126L10_MS405_sp114_mix2_ab102B-S10_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/181126L11_MS407_sp116_mix1_ab102A-S11_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/181126L12_MS407_sp116_mix1_ab102B-S12_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/181126L13_MS407_sp116_mix2_ab102A-S13_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/181126L14_MS407_sp116_mix2_ab102B-S14_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/181126L15_MS1_sp108_ab102B-S15_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/181126L16_MS407_sp108_ab102A-S16_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/181126L17_MS407_sp108_ab102B-S17_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L01_MS1_input-S01_A/181105L01_MS1_input-S01_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L01_MS1_input-S01_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L02_MS80_input-S02_A/181105L02_MS80_input-S02_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L02_MS80_input-S02_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L03_MS81_input-S03_A/181105L03_MS81_input-S03_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L03_MS81_input-S03_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L04_MS63_0nM_input-S04_A/181105L04_MS63_0nM_input-S04_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L04_MS63_0nM_input-S04_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L05_MS63_10nM_input-S05_A/181105L05_MS63_10nM_input-S05_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L05_MS63_10nM_input-S05_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L06_MS63_30nM_input-S06_A/181105L06_MS63_30nM_input-S06_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L06_MS63_30nM_input-S06_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L07_MS1_AB20-S07_A/181105L07_MS1_AB20-S07_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L07_MS1_AB20-S07_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L08_MS80_AB20-S08_A/181105L08_MS80_AB20-S08_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L08_MS80_AB20-S08_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L09_MS81_AB20-S09_A/181105L09_MS81_AB20-S09_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L09_MS81_AB20-S09_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L10_MS63_0nM_AB20-S10_A/181105L10_MS63_0nM_AB20-S10_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L11_MS63_10nM_AB20-S11_A/181105L11_MS63_10nM_AB20-S11_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L12_MS63_30nM_AB20-S12_A/181105L12_MS63_30nM_AB20-S12_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L13_MS1_AB21-S13_A/181105L13_MS1_AB21-S13_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L13_MS1_AB21-S13_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L14_MS80_AB21-S14_A/181105L14_MS80_AB21-S14_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L14_MS80_AB21-S14_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L15_MS81_AB21-S15_A/181105L15_MS81_AB21-S15_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L15_MS81_AB21-S15_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L16_MS63_0nM_AB21-S16_A/181105L16_MS63_0nM_AB21-S16_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L17_MS63_10nM_AB21-S17_A/181105L17_MS63_10nM_AB21-S17_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L18_MS63_30nM_AB21-S18_A/181105L18_MS63_30nM_AB21-S18_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L19_MS1_AB39-S19_A/181105L19_MS1_AB39-S19_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L19_MS1_AB39-S19_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L20_MS80_AB39-S20_A/181105L20_MS80_AB39-S20_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L20_MS80_AB39-S20_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L21_MS81_AB39-S21_A/181105L21_MS81_AB39-S21_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L21_MS81_AB39-S21_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L22_MS63_0nM_AB39-S22_A/181105L22_MS63_0nM_AB39-S22_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L23_MS63_10nM_AB39-S23_A/181105L23_MS63_10nM_AB39-S23_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L24_MS63_30nM_AB39-S24_A/181105L24_MS63_30nM_AB39-S24_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L25_MS1_AB41-S25_A/181105L25_MS1_AB41-S25_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L25_MS1_AB41-S25_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L26_MS80_AB41-S26_A/181105L26_MS80_AB41-S26_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L26_MS80_AB41-S26_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L27_MS81_AB41-S27_A/181105L27_MS81_AB41-S27_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L27_MS81_AB41-S27_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L28_MS63_0nM_AB41-S28_A/181105L28_MS63_0nM_AB41-S28_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L29_MS63_10nM_AB41-S29_A/181105L29_MS63_10nM_AB41-S29_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L30_MS63_30nM_AB41-S30_A/181105L30_MS63_30nM_AB41-S30_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L31_MS1_AB42-S31_A/181105L31_MS1_AB42-S31_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L31_MS1_AB42-S31_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L32_MS80_AB42-S32_A/181105L32_MS80_AB42-S32_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L32_MS80_AB42-S32_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L33_MS81_AB42-S33_A/181105L33_MS81_AB42-S33_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L33_MS81_AB42-S33_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L34_MS63_0nM_AB42-S34_A/181105L34_MS63_0nM_AB42-S34_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L35_MS63_10nM_AB42-S35_A/181105L35_MS63_10nM_AB42-S35_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L36_MS63_30nM_AB42-S36_A/181105L36_MS63_30nM_AB42-S36_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L37_MS1_AB43-S37_A/181105L37_MS1_AB43-S37_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L37_MS1_AB43-S37_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L38_MS80_AB43-S38_A/181105L38_MS80_AB43-S38_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L38_MS80_AB43-S38_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L39_MS81_AB43-S39_A/181105L39_MS81_AB43-S39_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L39_MS81_AB43-S39_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L40_MS63_0nM_AB43-S40_A/181105L40_MS63_0nM_AB43-S40_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L41_MS63_10nM_AB43-S41_A/181105L41_MS63_10nM_AB43-S41_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L42_MS63_30nM_AB43-S42_A/181105L42_MS63_30nM_AB43-S42_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L43_MS1_AB44-S43_A/181105L43_MS1_AB44-S43_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L43_MS1_AB44-S43_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L44_MS80_AB44-S44_A/181105L44_MS80_AB44-S44_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L44_MS80_AB44-S44_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L45_MS81_AB44-S45_A/181105L45_MS81_AB44-S45_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L45_MS81_AB44-S45_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L46_MS63_0nM_AB44-S46_A/181105L46_MS63_0nM_AB44-S46_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L47_MS63_10nM_AB44-S47_A/181105L47_MS63_10nM_AB44-S47_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L48_MS63_30nM_AB44-S48_A/181105L48_MS63_30nM_AB44-S48_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L49_MS1_AB45-S49_A/181105L49_MS1_AB45-S49_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L49_MS1_AB45-S49_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L50_MS80_AB45-S50_A/181105L50_MS80_AB45-S50_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L50_MS80_AB45-S50_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L51_MS81_AB45-S51_A/181105L51_MS81_AB45-S51_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L51_MS81_AB45-S51_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L52_MS63_0nM_AB45-S52_A/181105L52_MS63_0nM_AB45-S52_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L53_MS63_10nM_AB45-S53_A/181105L53_MS63_10nM_AB45-S53_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L54_MS63_30nM_AB45-S54_A/181105L54_MS63_30nM_AB45-S54_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L55_MS1_AB46-S55_A/181105L55_MS1_AB46-S55_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L55_MS1_AB46-S55_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L56_MS80_AB46-S56_A/181105L56_MS80_AB46-S56_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L56_MS80_AB46-S56_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L57_MS81_AB46-S57_A/181105L57_MS81_AB46-S57_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L57_MS81_AB46-S57_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L58_MS63_0nM_AB46-S58_A/181105L58_MS63_0nM_AB46-S58_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L59_MS63_10nM_AB46-S59_A/181105L59_MS63_10nM_AB46-S59_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L60_MS63_30nM_AB46-S60_A/181105L60_MS63_30nM_AB46-S60_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L61_MS1_AB47-S61_A/181105L61_MS1_AB47-S61_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L61_MS1_AB47-S61_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L62_MS80_AB47-S62_A/181105L62_MS80_AB47-S62_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L62_MS80_AB47-S62_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L63_MS81_AB47-S63_A/181105L63_MS81_AB47-S63_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L63_MS81_AB47-S63_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L64_MS63_0nM_AB47-S64_A/181105L64_MS63_0nM_AB47-S64_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L65_MS63_10nM_AB47-S65_A/181105L65_MS63_10nM_AB47-S65_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L66_MS63_30nM_AB47-S66_A/181105L66_MS63_30nM_AB47-S66_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L67_MS1_AB48-S67_A/181105L67_MS1_AB48-S67_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L67_MS1_AB48-S67_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L68_MS80_AB48-S68_A/181105L68_MS80_AB48-S68_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L68_MS80_AB48-S68_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L69_MS81_AB48-S69_A/181105L69_MS81_AB48-S69_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L69_MS81_AB48-S69_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L70_MS63_0nM_AB48-S70_A/181105L70_MS63_0nM_AB48-S70_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L71_MS63_10nM_AB48-S71_A/181105L71_MS63_10nM_AB48-S71_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L72_MS63_30nM_AB48-S72_A/181105L72_MS63_30nM_AB48-S72_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/181030L01-S18_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L01-S18_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/181030L02-S19_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L02-S19_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/181030L03-S20_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L03-S20_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/181030L04-S21_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L04-S21_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/181030L05-S22_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L05-S22_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/181030L06-S23_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L06-S23_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/181030L07-S24_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L07-S24_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/181030L08-S25_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L08-S25_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/181030L09-S26_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L09-S26_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/181030L10-S27_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L10-S27_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/181030L11-S28_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L11-S28_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/181030L12-S29_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L12-S29_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/181030L13-S30_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L13-S30_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/181030L14-S31_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L14-S31_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/181030L15-S32_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L15-S32_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/181030L16-S33_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L16-S33_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/181030L17-S34_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L17-S34_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/181030L18-S35_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L18-S35_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/181030L19-S36_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L19-S36_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/181126L01_MS405_sp114_mix1_input-S01_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/181126L02_MS405_sp114_mix2_input-S02_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/181126L03_MS407_sp116_mix1_input-S03_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/181126L04_MS407_sp116_mix2_input-S04_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/181126L05_MS1_sp108_input-S05_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L05_MS1_sp108_input-S05_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/181126L06_MS407_sp108_input-S06_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L06_MS407_sp108_input-S06_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/181126L07_MS405_sp114_mix1_ab102A-S07_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/181126L08_MS405_sp114_mix1_ab102B-S08_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/181126L09_MS405_sp114_mix2_ab102A-S09_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/181126L10_MS405_sp114_mix2_ab102B-S10_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/181126L11_MS407_sp116_mix1_ab102A-S11_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/181126L12_MS407_sp116_mix1_ab102B-S12_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/181126L13_MS407_sp116_mix2_ab102A-S13_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/181126L14_MS407_sp116_mix2_ab102B-S14_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/181126L15_MS1_sp108_ab102B-S15_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/181126L16_MS407_sp108_ab102A-S16_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/181126L17_MS407_sp108_ab102B-S17_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L01_MS1_input-S01_A/181105L01_MS1_input-S01_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L01_MS1_input-S01_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L02_MS80_input-S02_A/181105L02_MS80_input-S02_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L02_MS80_input-S02_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L03_MS81_input-S03_A/181105L03_MS81_input-S03_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L03_MS81_input-S03_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L04_MS63_0nM_input-S04_A/181105L04_MS63_0nM_input-S04_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L04_MS63_0nM_input-S04_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L05_MS63_10nM_input-S05_A/181105L05_MS63_10nM_input-S05_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L05_MS63_10nM_input-S05_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L06_MS63_30nM_input-S06_A/181105L06_MS63_30nM_input-S06_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L06_MS63_30nM_input-S06_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L07_MS1_AB20-S07_A/181105L07_MS1_AB20-S07_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L07_MS1_AB20-S07_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L08_MS80_AB20-S08_A/181105L08_MS80_AB20-S08_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L08_MS80_AB20-S08_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L09_MS81_AB20-S09_A/181105L09_MS81_AB20-S09_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L09_MS81_AB20-S09_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L10_MS63_0nM_AB20-S10_A/181105L10_MS63_0nM_AB20-S10_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L11_MS63_10nM_AB20-S11_A/181105L11_MS63_10nM_AB20-S11_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L12_MS63_30nM_AB20-S12_A/181105L12_MS63_30nM_AB20-S12_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L13_MS1_AB21-S13_A/181105L13_MS1_AB21-S13_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L13_MS1_AB21-S13_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L14_MS80_AB21-S14_A/181105L14_MS80_AB21-S14_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L14_MS80_AB21-S14_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L15_MS81_AB21-S15_A/181105L15_MS81_AB21-S15_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L15_MS81_AB21-S15_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L16_MS63_0nM_AB21-S16_A/181105L16_MS63_0nM_AB21-S16_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L17_MS63_10nM_AB21-S17_A/181105L17_MS63_10nM_AB21-S17_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L18_MS63_30nM_AB21-S18_A/181105L18_MS63_30nM_AB21-S18_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L19_MS1_AB39-S19_A/181105L19_MS1_AB39-S19_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L19_MS1_AB39-S19_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L20_MS80_AB39-S20_A/181105L20_MS80_AB39-S20_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L20_MS80_AB39-S20_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L21_MS81_AB39-S21_A/181105L21_MS81_AB39-S21_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L21_MS81_AB39-S21_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L22_MS63_0nM_AB39-S22_A/181105L22_MS63_0nM_AB39-S22_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L23_MS63_10nM_AB39-S23_A/181105L23_MS63_10nM_AB39-S23_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L24_MS63_30nM_AB39-S24_A/181105L24_MS63_30nM_AB39-S24_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L25_MS1_AB41-S25_A/181105L25_MS1_AB41-S25_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L25_MS1_AB41-S25_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L26_MS80_AB41-S26_A/181105L26_MS80_AB41-S26_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L26_MS80_AB41-S26_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L27_MS81_AB41-S27_A/181105L27_MS81_AB41-S27_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L27_MS81_AB41-S27_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L28_MS63_0nM_AB41-S28_A/181105L28_MS63_0nM_AB41-S28_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L29_MS63_10nM_AB41-S29_A/181105L29_MS63_10nM_AB41-S29_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L30_MS63_30nM_AB41-S30_A/181105L30_MS63_30nM_AB41-S30_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L31_MS1_AB42-S31_A/181105L31_MS1_AB42-S31_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L31_MS1_AB42-S31_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L32_MS80_AB42-S32_A/181105L32_MS80_AB42-S32_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L32_MS80_AB42-S32_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L33_MS81_AB42-S33_A/181105L33_MS81_AB42-S33_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L33_MS81_AB42-S33_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L34_MS63_0nM_AB42-S34_A/181105L34_MS63_0nM_AB42-S34_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L35_MS63_10nM_AB42-S35_A/181105L35_MS63_10nM_AB42-S35_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L36_MS63_30nM_AB42-S36_A/181105L36_MS63_30nM_AB42-S36_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L37_MS1_AB43-S37_A/181105L37_MS1_AB43-S37_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L37_MS1_AB43-S37_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L38_MS80_AB43-S38_A/181105L38_MS80_AB43-S38_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L38_MS80_AB43-S38_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L39_MS81_AB43-S39_A/181105L39_MS81_AB43-S39_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L39_MS81_AB43-S39_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L40_MS63_0nM_AB43-S40_A/181105L40_MS63_0nM_AB43-S40_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L41_MS63_10nM_AB43-S41_A/181105L41_MS63_10nM_AB43-S41_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L42_MS63_30nM_AB43-S42_A/181105L42_MS63_30nM_AB43-S42_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L43_MS1_AB44-S43_A/181105L43_MS1_AB44-S43_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L43_MS1_AB44-S43_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L44_MS80_AB44-S44_A/181105L44_MS80_AB44-S44_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L44_MS80_AB44-S44_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L45_MS81_AB44-S45_A/181105L45_MS81_AB44-S45_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L45_MS81_AB44-S45_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L46_MS63_0nM_AB44-S46_A/181105L46_MS63_0nM_AB44-S46_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L47_MS63_10nM_AB44-S47_A/181105L47_MS63_10nM_AB44-S47_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L48_MS63_30nM_AB44-S48_A/181105L48_MS63_30nM_AB44-S48_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L49_MS1_AB45-S49_A/181105L49_MS1_AB45-S49_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L49_MS1_AB45-S49_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L50_MS80_AB45-S50_A/181105L50_MS80_AB45-S50_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L50_MS80_AB45-S50_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L51_MS81_AB45-S51_A/181105L51_MS81_AB45-S51_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L51_MS81_AB45-S51_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L52_MS63_0nM_AB45-S52_A/181105L52_MS63_0nM_AB45-S52_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L53_MS63_10nM_AB45-S53_A/181105L53_MS63_10nM_AB45-S53_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L54_MS63_30nM_AB45-S54_A/181105L54_MS63_30nM_AB45-S54_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L55_MS1_AB46-S55_A/181105L55_MS1_AB46-S55_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L55_MS1_AB46-S55_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L56_MS80_AB46-S56_A/181105L56_MS80_AB46-S56_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L56_MS80_AB46-S56_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L57_MS81_AB46-S57_A/181105L57_MS81_AB46-S57_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L57_MS81_AB46-S57_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L58_MS63_0nM_AB46-S58_A/181105L58_MS63_0nM_AB46-S58_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L59_MS63_10nM_AB46-S59_A/181105L59_MS63_10nM_AB46-S59_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L60_MS63_30nM_AB46-S60_A/181105L60_MS63_30nM_AB46-S60_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L61_MS1_AB47-S61_A/181105L61_MS1_AB47-S61_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L61_MS1_AB47-S61_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L62_MS80_AB47-S62_A/181105L62_MS80_AB47-S62_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L62_MS80_AB47-S62_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L63_MS81_AB47-S63_A/181105L63_MS81_AB47-S63_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L63_MS81_AB47-S63_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L64_MS63_0nM_AB47-S64_A/181105L64_MS63_0nM_AB47-S64_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L65_MS63_10nM_AB47-S65_A/181105L65_MS63_10nM_AB47-S65_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L66_MS63_30nM_AB47-S66_A/181105L66_MS63_30nM_AB47-S66_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L67_MS1_AB48-S67_A/181105L67_MS1_AB48-S67_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L67_MS1_AB48-S67_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L68_MS80_AB48-S68_A/181105L68_MS80_AB48-S68_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L68_MS80_AB48-S68_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L69_MS81_AB48-S69_A/181105L69_MS81_AB48-S69_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L69_MS81_AB48-S69_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L70_MS63_0nM_AB48-S70_A/181105L70_MS63_0nM_AB48-S70_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L71_MS63_10nM_AB48-S71_A/181105L71_MS63_10nM_AB48-S71_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L72_MS63_30nM_AB48-S72_A/181105L72_MS63_30nM_AB48-S72_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.1x36mers.unique.nochrM.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/181030L01-S18_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L01-S18_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/181030L02-S19_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L02-S19_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/181030L03-S20_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L03-S20_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/181030L04-S21_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L04-S21_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/181030L05-S22_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L05-S22_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/181030L06-S23_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L06-S23_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/181030L07-S24_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L07-S24_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/181030L08-S25_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L08-S25_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/181030L09-S26_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L09-S26_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/181030L10-S27_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L10-S27_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/181030L11-S28_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L11-S28_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/181030L12-S29_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L12-S29_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/181030L13-S30_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L13-S30_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/181030L14-S31_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L14-S31_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/181030L15-S32_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L15-S32_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/181030L16-S33_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L16-S33_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/181030L17-S34_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L17-S34_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/181030L18-S35_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L18-S35_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/181030L19-S36_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181030L19-S36_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/181126L01_MS405_sp114_mix1_input-S01_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/181126L02_MS405_sp114_mix2_input-S02_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/181126L03_MS407_sp116_mix1_input-S03_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/181126L04_MS407_sp116_mix2_input-S04_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/181126L05_MS1_sp108_input-S05_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L05_MS1_sp108_input-S05_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/181126L06_MS407_sp108_input-S06_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L06_MS407_sp108_input-S06_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/181126L07_MS405_sp114_mix1_ab102A-S07_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/181126L08_MS405_sp114_mix1_ab102B-S08_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/181126L09_MS405_sp114_mix2_ab102A-S09_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/181126L10_MS405_sp114_mix2_ab102B-S10_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/181126L11_MS407_sp116_mix1_ab102A-S11_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/181126L12_MS407_sp116_mix1_ab102B-S12_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/181126L13_MS407_sp116_mix2_ab102A-S13_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/181126L14_MS407_sp116_mix2_ab102B-S14_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/181126L15_MS1_sp108_ab102B-S15_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/181126L16_MS407_sp108_ab102A-S16_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/181126L17_MS407_sp108_ab102B-S17_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream500bp.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L01_MS1_input-S01_A/181105L01_MS1_input-S01_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L01_MS1_input-S01_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L02_MS80_input-S02_A/181105L02_MS80_input-S02_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L02_MS80_input-S02_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L03_MS81_input-S03_A/181105L03_MS81_input-S03_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L03_MS81_input-S03_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L04_MS63_0nM_input-S04_A/181105L04_MS63_0nM_input-S04_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L04_MS63_0nM_input-S04_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L05_MS63_10nM_input-S05_A/181105L05_MS63_10nM_input-S05_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L05_MS63_10nM_input-S05_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L06_MS63_30nM_input-S06_A/181105L06_MS63_30nM_input-S06_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L06_MS63_30nM_input-S06_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L07_MS1_AB20-S07_A/181105L07_MS1_AB20-S07_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L07_MS1_AB20-S07_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L08_MS80_AB20-S08_A/181105L08_MS80_AB20-S08_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L08_MS80_AB20-S08_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L09_MS81_AB20-S09_A/181105L09_MS81_AB20-S09_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L09_MS81_AB20-S09_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L10_MS63_0nM_AB20-S10_A/181105L10_MS63_0nM_AB20-S10_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L11_MS63_10nM_AB20-S11_A/181105L11_MS63_10nM_AB20-S11_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L12_MS63_30nM_AB20-S12_A/181105L12_MS63_30nM_AB20-S12_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L13_MS1_AB21-S13_A/181105L13_MS1_AB21-S13_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L13_MS1_AB21-S13_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L14_MS80_AB21-S14_A/181105L14_MS80_AB21-S14_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L14_MS80_AB21-S14_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L15_MS81_AB21-S15_A/181105L15_MS81_AB21-S15_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L15_MS81_AB21-S15_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L16_MS63_0nM_AB21-S16_A/181105L16_MS63_0nM_AB21-S16_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L17_MS63_10nM_AB21-S17_A/181105L17_MS63_10nM_AB21-S17_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L18_MS63_30nM_AB21-S18_A/181105L18_MS63_30nM_AB21-S18_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L19_MS1_AB39-S19_A/181105L19_MS1_AB39-S19_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L19_MS1_AB39-S19_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L20_MS80_AB39-S20_A/181105L20_MS80_AB39-S20_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L20_MS80_AB39-S20_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L21_MS81_AB39-S21_A/181105L21_MS81_AB39-S21_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L21_MS81_AB39-S21_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L22_MS63_0nM_AB39-S22_A/181105L22_MS63_0nM_AB39-S22_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L23_MS63_10nM_AB39-S23_A/181105L23_MS63_10nM_AB39-S23_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L24_MS63_30nM_AB39-S24_A/181105L24_MS63_30nM_AB39-S24_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L25_MS1_AB41-S25_A/181105L25_MS1_AB41-S25_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L25_MS1_AB41-S25_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L26_MS80_AB41-S26_A/181105L26_MS80_AB41-S26_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L26_MS80_AB41-S26_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L27_MS81_AB41-S27_A/181105L27_MS81_AB41-S27_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L27_MS81_AB41-S27_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L28_MS63_0nM_AB41-S28_A/181105L28_MS63_0nM_AB41-S28_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L29_MS63_10nM_AB41-S29_A/181105L29_MS63_10nM_AB41-S29_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L30_MS63_30nM_AB41-S30_A/181105L30_MS63_30nM_AB41-S30_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L31_MS1_AB42-S31_A/181105L31_MS1_AB42-S31_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L31_MS1_AB42-S31_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L32_MS80_AB42-S32_A/181105L32_MS80_AB42-S32_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L32_MS80_AB42-S32_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L33_MS81_AB42-S33_A/181105L33_MS81_AB42-S33_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L33_MS81_AB42-S33_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L34_MS63_0nM_AB42-S34_A/181105L34_MS63_0nM_AB42-S34_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L35_MS63_10nM_AB42-S35_A/181105L35_MS63_10nM_AB42-S35_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L36_MS63_30nM_AB42-S36_A/181105L36_MS63_30nM_AB42-S36_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L37_MS1_AB43-S37_A/181105L37_MS1_AB43-S37_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L37_MS1_AB43-S37_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L38_MS80_AB43-S38_A/181105L38_MS80_AB43-S38_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L38_MS80_AB43-S38_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L39_MS81_AB43-S39_A/181105L39_MS81_AB43-S39_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L39_MS81_AB43-S39_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L40_MS63_0nM_AB43-S40_A/181105L40_MS63_0nM_AB43-S40_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L41_MS63_10nM_AB43-S41_A/181105L41_MS63_10nM_AB43-S41_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L42_MS63_30nM_AB43-S42_A/181105L42_MS63_30nM_AB43-S42_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L43_MS1_AB44-S43_A/181105L43_MS1_AB44-S43_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L43_MS1_AB44-S43_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L44_MS80_AB44-S44_A/181105L44_MS80_AB44-S44_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L44_MS80_AB44-S44_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L45_MS81_AB44-S45_A/181105L45_MS81_AB44-S45_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L45_MS81_AB44-S45_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L46_MS63_0nM_AB44-S46_A/181105L46_MS63_0nM_AB44-S46_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L47_MS63_10nM_AB44-S47_A/181105L47_MS63_10nM_AB44-S47_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L48_MS63_30nM_AB44-S48_A/181105L48_MS63_30nM_AB44-S48_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L49_MS1_AB45-S49_A/181105L49_MS1_AB45-S49_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L49_MS1_AB45-S49_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L50_MS80_AB45-S50_A/181105L50_MS80_AB45-S50_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L50_MS80_AB45-S50_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L51_MS81_AB45-S51_A/181105L51_MS81_AB45-S51_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L51_MS81_AB45-S51_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L52_MS63_0nM_AB45-S52_A/181105L52_MS63_0nM_AB45-S52_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L53_MS63_10nM_AB45-S53_A/181105L53_MS63_10nM_AB45-S53_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L54_MS63_30nM_AB45-S54_A/181105L54_MS63_30nM_AB45-S54_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L55_MS1_AB46-S55_A/181105L55_MS1_AB46-S55_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L55_MS1_AB46-S55_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L56_MS80_AB46-S56_A/181105L56_MS80_AB46-S56_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L56_MS80_AB46-S56_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L57_MS81_AB46-S57_A/181105L57_MS81_AB46-S57_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L57_MS81_AB46-S57_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L58_MS63_0nM_AB46-S58_A/181105L58_MS63_0nM_AB46-S58_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L59_MS63_10nM_AB46-S59_A/181105L59_MS63_10nM_AB46-S59_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L60_MS63_30nM_AB46-S60_A/181105L60_MS63_30nM_AB46-S60_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L61_MS1_AB47-S61_A/181105L61_MS1_AB47-S61_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L61_MS1_AB47-S61_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L62_MS80_AB47-S62_A/181105L62_MS80_AB47-S62_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L62_MS80_AB47-S62_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L63_MS81_AB47-S63_A/181105L63_MS81_AB47-S63_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L63_MS81_AB47-S63_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L64_MS63_0nM_AB47-S64_A/181105L64_MS63_0nM_AB47-S64_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L65_MS63_10nM_AB47-S65_A/181105L65_MS63_10nM_AB47-S65_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L66_MS63_30nM_AB47-S66_A/181105L66_MS63_30nM_AB47-S66_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L67_MS1_AB48-S67_A/181105L67_MS1_AB48-S67_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L67_MS1_AB48-S67_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L68_MS80_AB48-S68_A/181105L68_MS80_AB48-S68_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L68_MS80_AB48-S68_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L69_MS81_AB48-S69_A/181105L69_MS81_AB48-S69_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L69_MS81_AB48-S69_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L70_MS63_0nM_AB48-S70_A/181105L70_MS63_0nM_AB48-S70_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L71_MS63_10nM_AB48-S71_A/181105L71_MS63_10nM_AB48-S71_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L72_MS63_30nM_AB48-S72_A/181105L72_MS63_30nM_AB48-S72_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream500bp.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/181030L01-S18_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L01-S18_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/181030L02-S19_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L02-S19_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/181030L03-S20_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L03-S20_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/181030L04-S21_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L04-S21_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/181030L05-S22_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L05-S22_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/181030L06-S23_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L06-S23_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/181030L07-S24_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L07-S24_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/181030L08-S25_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L08-S25_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/181030L09-S26_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L09-S26_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/181030L10-S27_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L10-S27_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/181030L11-S28_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L11-S28_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/181030L12-S29_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L12-S29_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/181030L13-S30_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L13-S30_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/181030L14-S31_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L14-S31_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/181030L15-S32_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L15-S32_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/181030L16-S33_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L16-S33_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/181030L17-S34_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L17-S34_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/181030L18-S35_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L18-S35_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/181030L19-S36_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181030L19-S36_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/181126L01_MS405_sp114_mix1_input-S01_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/181126L02_MS405_sp114_mix2_input-S02_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/181126L03_MS407_sp116_mix1_input-S03_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/181126L04_MS407_sp116_mix2_input-S04_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/181126L05_MS1_sp108_input-S05_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L05_MS1_sp108_input-S05_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/181126L06_MS407_sp108_input-S06_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L06_MS407_sp108_input-S06_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/181126L07_MS405_sp114_mix1_ab102A-S07_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/181126L08_MS405_sp114_mix1_ab102B-S08_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/181126L09_MS405_sp114_mix2_ab102A-S09_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/181126L10_MS405_sp114_mix2_ab102B-S10_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/181126L11_MS407_sp116_mix1_ab102A-S11_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/181126L12_MS407_sp116_mix1_ab102B-S12_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/181126L13_MS407_sp116_mix2_ab102A-S13_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/181126L14_MS407_sp116_mix2_ab102B-S14_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/181126L15_MS1_sp108_ab102B-S15_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/181126L16_MS407_sp108_ab102A-S16_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.fixed.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/181126L17_MS407_sp108_ab102B-S17_B.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes TSS-upstream1000bp.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L01_MS1_input-S01_A/181105L01_MS1_input-S01_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L01_MS1_input-S01_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L02_MS80_input-S02_A/181105L02_MS80_input-S02_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L02_MS80_input-S02_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L03_MS81_input-S03_A/181105L03_MS81_input-S03_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L03_MS81_input-S03_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L04_MS63_0nM_input-S04_A/181105L04_MS63_0nM_input-S04_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L04_MS63_0nM_input-S04_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L05_MS63_10nM_input-S05_A/181105L05_MS63_10nM_input-S05_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L05_MS63_10nM_input-S05_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L06_MS63_30nM_input-S06_A/181105L06_MS63_30nM_input-S06_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L06_MS63_30nM_input-S06_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L07_MS1_AB20-S07_A/181105L07_MS1_AB20-S07_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L07_MS1_AB20-S07_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L08_MS80_AB20-S08_A/181105L08_MS80_AB20-S08_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L08_MS80_AB20-S08_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L09_MS81_AB20-S09_A/181105L09_MS81_AB20-S09_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L09_MS81_AB20-S09_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L10_MS63_0nM_AB20-S10_A/181105L10_MS63_0nM_AB20-S10_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L10_MS63_0nM_AB20-S10_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L11_MS63_10nM_AB20-S11_A/181105L11_MS63_10nM_AB20-S11_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L11_MS63_10nM_AB20-S11_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L12_MS63_30nM_AB20-S12_A/181105L12_MS63_30nM_AB20-S12_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L12_MS63_30nM_AB20-S12_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L13_MS1_AB21-S13_A/181105L13_MS1_AB21-S13_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L13_MS1_AB21-S13_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L14_MS80_AB21-S14_A/181105L14_MS80_AB21-S14_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L14_MS80_AB21-S14_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L15_MS81_AB21-S15_A/181105L15_MS81_AB21-S15_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L15_MS81_AB21-S15_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L16_MS63_0nM_AB21-S16_A/181105L16_MS63_0nM_AB21-S16_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L16_MS63_0nM_AB21-S16_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L17_MS63_10nM_AB21-S17_A/181105L17_MS63_10nM_AB21-S17_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L17_MS63_10nM_AB21-S17_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L18_MS63_30nM_AB21-S18_A/181105L18_MS63_30nM_AB21-S18_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L18_MS63_30nM_AB21-S18_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L19_MS1_AB39-S19_A/181105L19_MS1_AB39-S19_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L19_MS1_AB39-S19_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L20_MS80_AB39-S20_A/181105L20_MS80_AB39-S20_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L20_MS80_AB39-S20_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L21_MS81_AB39-S21_A/181105L21_MS81_AB39-S21_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L21_MS81_AB39-S21_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L22_MS63_0nM_AB39-S22_A/181105L22_MS63_0nM_AB39-S22_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L22_MS63_0nM_AB39-S22_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L23_MS63_10nM_AB39-S23_A/181105L23_MS63_10nM_AB39-S23_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L23_MS63_10nM_AB39-S23_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L24_MS63_30nM_AB39-S24_A/181105L24_MS63_30nM_AB39-S24_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L24_MS63_30nM_AB39-S24_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L25_MS1_AB41-S25_A/181105L25_MS1_AB41-S25_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L25_MS1_AB41-S25_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L26_MS80_AB41-S26_A/181105L26_MS80_AB41-S26_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L26_MS80_AB41-S26_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L27_MS81_AB41-S27_A/181105L27_MS81_AB41-S27_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L27_MS81_AB41-S27_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L28_MS63_0nM_AB41-S28_A/181105L28_MS63_0nM_AB41-S28_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L28_MS63_0nM_AB41-S28_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L29_MS63_10nM_AB41-S29_A/181105L29_MS63_10nM_AB41-S29_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L29_MS63_10nM_AB41-S29_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L30_MS63_30nM_AB41-S30_A/181105L30_MS63_30nM_AB41-S30_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L30_MS63_30nM_AB41-S30_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L31_MS1_AB42-S31_A/181105L31_MS1_AB42-S31_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L31_MS1_AB42-S31_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L32_MS80_AB42-S32_A/181105L32_MS80_AB42-S32_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L32_MS80_AB42-S32_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L33_MS81_AB42-S33_A/181105L33_MS81_AB42-S33_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L33_MS81_AB42-S33_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L34_MS63_0nM_AB42-S34_A/181105L34_MS63_0nM_AB42-S34_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L34_MS63_0nM_AB42-S34_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L35_MS63_10nM_AB42-S35_A/181105L35_MS63_10nM_AB42-S35_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L35_MS63_10nM_AB42-S35_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L36_MS63_30nM_AB42-S36_A/181105L36_MS63_30nM_AB42-S36_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L36_MS63_30nM_AB42-S36_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L37_MS1_AB43-S37_A/181105L37_MS1_AB43-S37_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L37_MS1_AB43-S37_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L38_MS80_AB43-S38_A/181105L38_MS80_AB43-S38_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L38_MS80_AB43-S38_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L39_MS81_AB43-S39_A/181105L39_MS81_AB43-S39_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L39_MS81_AB43-S39_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L40_MS63_0nM_AB43-S40_A/181105L40_MS63_0nM_AB43-S40_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L40_MS63_0nM_AB43-S40_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L41_MS63_10nM_AB43-S41_A/181105L41_MS63_10nM_AB43-S41_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L41_MS63_10nM_AB43-S41_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L42_MS63_30nM_AB43-S42_A/181105L42_MS63_30nM_AB43-S42_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L42_MS63_30nM_AB43-S42_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L43_MS1_AB44-S43_A/181105L43_MS1_AB44-S43_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L43_MS1_AB44-S43_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L44_MS80_AB44-S44_A/181105L44_MS80_AB44-S44_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L44_MS80_AB44-S44_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L45_MS81_AB44-S45_A/181105L45_MS81_AB44-S45_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L45_MS81_AB44-S45_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L46_MS63_0nM_AB44-S46_A/181105L46_MS63_0nM_AB44-S46_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L46_MS63_0nM_AB44-S46_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L47_MS63_10nM_AB44-S47_A/181105L47_MS63_10nM_AB44-S47_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L47_MS63_10nM_AB44-S47_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L48_MS63_30nM_AB44-S48_A/181105L48_MS63_30nM_AB44-S48_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L48_MS63_30nM_AB44-S48_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L49_MS1_AB45-S49_A/181105L49_MS1_AB45-S49_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L49_MS1_AB45-S49_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L50_MS80_AB45-S50_A/181105L50_MS80_AB45-S50_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L50_MS80_AB45-S50_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L51_MS81_AB45-S51_A/181105L51_MS81_AB45-S51_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L51_MS81_AB45-S51_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L52_MS63_0nM_AB45-S52_A/181105L52_MS63_0nM_AB45-S52_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L52_MS63_0nM_AB45-S52_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L53_MS63_10nM_AB45-S53_A/181105L53_MS63_10nM_AB45-S53_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L53_MS63_10nM_AB45-S53_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L54_MS63_30nM_AB45-S54_A/181105L54_MS63_30nM_AB45-S54_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L54_MS63_30nM_AB45-S54_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L55_MS1_AB46-S55_A/181105L55_MS1_AB46-S55_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L55_MS1_AB46-S55_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L56_MS80_AB46-S56_A/181105L56_MS80_AB46-S56_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L56_MS80_AB46-S56_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L57_MS81_AB46-S57_A/181105L57_MS81_AB46-S57_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L57_MS81_AB46-S57_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L58_MS63_0nM_AB46-S58_A/181105L58_MS63_0nM_AB46-S58_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L58_MS63_0nM_AB46-S58_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L59_MS63_10nM_AB46-S59_A/181105L59_MS63_10nM_AB46-S59_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L59_MS63_10nM_AB46-S59_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L60_MS63_30nM_AB46-S60_A/181105L60_MS63_30nM_AB46-S60_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L60_MS63_30nM_AB46-S60_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L61_MS1_AB47-S61_A/181105L61_MS1_AB47-S61_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L61_MS1_AB47-S61_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L62_MS80_AB47-S62_A/181105L62_MS80_AB47-S62_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L62_MS80_AB47-S62_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L63_MS81_AB47-S63_A/181105L63_MS81_AB47-S63_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L63_MS81_AB47-S63_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L64_MS63_0nM_AB47-S64_A/181105L64_MS63_0nM_AB47-S64_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L64_MS63_0nM_AB47-S64_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L65_MS63_10nM_AB47-S65_A/181105L65_MS63_10nM_AB47-S65_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L65_MS63_10nM_AB47-S65_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L66_MS63_30nM_AB47-S66_A/181105L66_MS63_30nM_AB47-S66_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L66_MS63_30nM_AB47-S66_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L67_MS1_AB48-S67_A/181105L67_MS1_AB48-S67_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L67_MS1_AB48-S67_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L68_MS80_AB48-S68_A/181105L68_MS80_AB48-S68_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L68_MS80_AB48-S68_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L69_MS81_AB48-S69_A/181105L69_MS81_AB48-S69_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L69_MS81_AB48-S69_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L70_MS63_0nM_AB48-S70_A/181105L70_MS63_0nM_AB48-S70_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L70_MS63_0nM_AB48-S70_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L71_MS63_10nM_AB48-S71_A/181105L71_MS63_10nM_AB48-S71_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L71_MS63_10nM_AB48-S71_A.1x36mers.unique.nochrM.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream1000bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181105L72_MS63_30nM_AB48-S72_A/181105L72_MS63_30nM_AB48-S72_A.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.chrom.sizes TSS-upstream1000bp.2019-01-03-181105L72_MS63_30nM_AB48-S72_A.1x36mers.unique.nochrM.RPKM &