python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L49_MS207-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L49_MS207-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L50_MS249-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L50_MS249-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L51_MS250-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L51_MS250-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L52_MS297-RAPA_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L52_MS297-RAPA_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L53_MS250-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L53_MS250-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L54_MS297-DMSO_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L54_MS297-DMSO_AB20-H3.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L01_MS55_A_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L02_MS55_B_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L03_MS55_C_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L04_MS55_D_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L05_MS55_E_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L06_MS55_F_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L19_MS55_A_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L20_MS55_B_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L21_MS55_C_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L22_MS55_D_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L23_MS55_E_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L24_MS55_F_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L25_MS55_A_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L26_MS55_B_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L27_MS55_C_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L28_MS55_D_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L29_MS55_E_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L30_MS55_F_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L55_MS283.2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L56_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L57_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L58_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L59_MS88_FrA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L60_MS88_FrB_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L61_MS88_FrC_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L62_MS88_FrD_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM  -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L01_MS55_A_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L01_MS55_A_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L02_MS55_B_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L02_MS55_B_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L03_MS55_C_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L03_MS55_C_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L04_MS55_D_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L04_MS55_D_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L05_MS55_E_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L05_MS55_E_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L06_MS55_F_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L06_MS55_F_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L07_MS55_A_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L07_MS55_A_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L08_MS55_B_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L08_MS55_B_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L09_MS55_C_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L09_MS55_C_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L10_MS55_D_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L10_MS55_D_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L11_MS55_E_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L11_MS55_E_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L12_MS55_F_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L12_MS55_F_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L13_MS55_A_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L14_MS55_B_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L15_MS55_C_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L16_MS55_D_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L17_MS55_E_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L18_MS55_F_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L19_MS55_A_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L19_MS55_A_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L20_MS55_B_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L20_MS55_B_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L21_MS55_C_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L21_MS55_C_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L22_MS55_D_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L22_MS55_D_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L23_MS55_E_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L23_MS55_E_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L24_MS55_F_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L24_MS55_F_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L25_MS55_A_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L25_MS55_A_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L26_MS55_B_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L26_MS55_B_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L27_MS55_C_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L27_MS55_C_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L28_MS55_D_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L28_MS55_D_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L29_MS55_E_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L29_MS55_E_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L30_MS55_F_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L30_MS55_F_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L31_MS55_A_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L31_MS55_A_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L32_MS55_B_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L32_MS55_B_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L33_MS55_C_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L33_MS55_C_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L34_MS55_D_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L34_MS55_D_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L35_MS55_E_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L35_MS55_E_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L36_MS55_F_AB48-H3K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L36_MS55_F_AB48-H3K36me3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L55_MS283.2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L55_MS283.2_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L56_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L56_MS286_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L57_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L57_MS287_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L58_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L58_MS288_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L59_MS88_FrA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L59_MS88_FrA_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L60_MS88_FrB_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L60_MS88_FrB_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L61_MS88_FrC_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L61_MS88_FrC_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L62_MS88_FrD_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L62_MS88_FrD_input.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L63_MS88_FrA_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L64_MS88_FrB_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L65_MS88_FrC_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L66_MS88_FrD_AB01-Rpb1.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L67_MS88_FrA_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L68_MS88_FrB_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L69_MS88_FrC_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L70_MS88_FrD_AB04-Rpb1S2P.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L71_MS88_FrA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L71_MS88_FrA_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L72_MS88_FrB_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L72_MS88_FrB_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L73_MS88_FrC_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L73_MS88_FrC_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L74_MS88_FrD_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L74_MS88_FrD_AB20-H3.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L75_MS88_FrA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L75_MS88_FrA_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L76_MS88_FrB_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L76_MS88_FrB_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L77_MS88_FrC_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L77_MS88_FrC_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L78_MS88_FrD_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L78_MS88_FrD_AB21-H4.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-10-07-190923L83_MS88_FrD_AB01-Rpb1_R.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes &