python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L01-MS521-AB101.2x36mers.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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L02-MS522-AB101.2x36mers.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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L03-MS523-AB101.2x36mers.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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L04-MS524-AB101.2x36mers.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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L05-MS527-AB101.2x36mers.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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L06-MS528-AB101.2x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L02-MK737-AB101.2x36mers.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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L03-MK842-AB101.2x36mers.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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L04-MK843-AB101.2x36mers.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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L05-MK844-AB101.2x36mers.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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L06-MK845-AB101.2x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L01-MS521-AB101.2x36mers.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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L02-MS522-AB101.2x36mers.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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L03-MS523-AB101.2x36mers.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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L04-MS524-AB101.2x36mers.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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L05-MS527-AB101.2x36mers.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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L06-MS528-AB101.2x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L02-MK737-AB101.2x36mers.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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L03-MK842-AB101.2x36mers.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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L04-MK843-AB101.2x36mers.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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L05-MK844-AB101.2x36mers.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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L06-MK845-AB101.2x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L01-MS521-AB101.2x36mers.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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L02-MS522-AB101.2x36mers.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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L03-MS523-AB101.2x36mers.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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L04-MS524-AB101.2x36mers.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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L05-MS527-AB101.2x36mers.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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L06-MS528-AB101.2x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L02-MK737-AB101.2x36mers.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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L03-MK842-AB101.2x36mers.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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L04-MK843-AB101.2x36mers.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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L05-MK844-AB101.2x36mers.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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L06-MK845-AB101.2x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L01-MS521-AB101.2x36mers.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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L02-MS522-AB101.2x36mers.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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L03-MS523-AB101.2x36mers.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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L04-MS524-AB101.2x36mers.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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L05-MS527-AB101.2x36mers.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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L06-MS528-AB101.2x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L02-MK737-AB101.2x36mers.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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L03-MK842-AB101.2x36mers.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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L04-MK843-AB101.2x36mers.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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L05-MK844-AB101.2x36mers.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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L06-MK845-AB101.2x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L01-MS521-AB101.1x36mers.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.sacCer3.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L02-MS522-AB101.1x36mers.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.sacCer3.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L03-MS523-AB101.1x36mers.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.sacCer3.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L04-MS524-AB101.1x36mers.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.sacCer3.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L05-MS527-AB101.1x36mers.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.sacCer3.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L06-MS528-AB101.1x36mers.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.sacCer3.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.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.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.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.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.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.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.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.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.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.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.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.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.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.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.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.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.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.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.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.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.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.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.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.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.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.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.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.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.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.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.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.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L02-MK737-AB101.1x36mers.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.sacCer3.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L03-MK842-AB101.1x36mers.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.sacCer3.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L04-MK843-AB101.1x36mers.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.sacCer3.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L05-MK844-AB101.1x36mers.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.sacCer3.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L06-MK845-AB101.1x36mers.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.sacCer3.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.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.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.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.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.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.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.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.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L01-MS521-AB101.1x36mers.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.sacCer3.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L02-MS522-AB101.1x36mers.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.sacCer3.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L03-MS523-AB101.1x36mers.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.sacCer3.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L04-MS524-AB101.1x36mers.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.sacCer3.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L05-MS527-AB101.1x36mers.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.sacCer3.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191103L06-MS528-AB101.1x36mers.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.sacCer3.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.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.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.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.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.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.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.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.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.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.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.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.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.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.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.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.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.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.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.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.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.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.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.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.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.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.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.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.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.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.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.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.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L02-MK737-AB101.1x36mers.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.sacCer3.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L03-MK842-AB101.1x36mers.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.sacCer3.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L04-MK843-AB101.1x36mers.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.sacCer3.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L05-MK844-AB101.1x36mers.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.sacCer3.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L06-MK845-AB101.1x36mers.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.sacCer3.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.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.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.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.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.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.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.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.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L01-MS521-AB101.1x36mers.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.sacCer3.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L02-MS522-AB101.1x36mers.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.sacCer3.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L03-MS523-AB101.1x36mers.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.sacCer3.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L04-MS524-AB101.1x36mers.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.sacCer3.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L05-MS527-AB101.1x36mers.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.sacCer3.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L06-MS528-AB101.1x36mers.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.sacCer3.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.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.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.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.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.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.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.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.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.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.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.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.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.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.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.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.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.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.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.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.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.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.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.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.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.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.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.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.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.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.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.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.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L02-MK737-AB101.1x36mers.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.sacCer3.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L03-MK842-AB101.1x36mers.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.sacCer3.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L04-MK843-AB101.1x36mers.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.sacCer3.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L05-MK844-AB101.1x36mers.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.sacCer3.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L06-MK845-AB101.1x36mers.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.sacCer3.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.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.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.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.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.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.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.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.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L01-MS521-AB101.1x36mers.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.sacCer3.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L02-MS522-AB101.1x36mers.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.sacCer3.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L03-MS523-AB101.1x36mers.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.sacCer3.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L04-MS524-AB101.1x36mers.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.sacCer3.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L05-MS527-AB101.1x36mers.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.sacCer3.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191103L06-MS528-AB101.1x36mers.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.sacCer3.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.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.sacCer3.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L01-MS207-RAPA-060-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.sacCer3.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L02-MS289-RAPA-060-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.sacCer3.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L03-MS290-RAPA-000-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.sacCer3.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L04-MS290-RAPA-020-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.sacCer3.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L05-MS290-RAPA-040-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.sacCer3.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L06-MS290-RAPA-060-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.sacCer3.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L07-MS290-RAPA-080-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.sacCer3.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L08-MS290-RAPA-100-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.sacCer3.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.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.sacCer3.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.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.sacCer3.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.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.sacCer3.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.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.sacCer3.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.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.sacCer3.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.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.sacCer3.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.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.sacCer3.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.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.sacCer3.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.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.sacCer3.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.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.sacCer3.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.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.sacCer3.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.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.sacCer3.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.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.sacCer3.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.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.sacCer3.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.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.sacCer3.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.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.sacCer3.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.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.sacCer3.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.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.sacCer3.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.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.sacCer3.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L02-MK737-AB101.1x36mers.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.sacCer3.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L03-MK842-AB101.1x36mers.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.sacCer3.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L04-MK843-AB101.1x36mers.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.sacCer3.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L05-MK844-AB101.1x36mers.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.sacCer3.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L06-MK845-AB101.1x36mers.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.sacCer3.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.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.sacCer3.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.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.sacCer3.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.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.sacCer3.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.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.sacCer3.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+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.2020-01-03-191103L01-MS521-AB101.2x36mers.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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+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.2020-01-03-191103L02-MS522-AB101.2x36mers.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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+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.2020-01-03-191103L03-MS523-AB101.2x36mers.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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+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.2020-01-03-191103L04-MS524-AB101.2x36mers.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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+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.2020-01-03-191103L05-MS527-AB101.2x36mers.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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+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.2020-01-03-191103L06-MS528-AB101.2x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+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.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+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.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+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.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+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.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+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.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+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.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+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.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+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.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+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.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+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.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+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.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+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.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+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.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+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.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+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.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+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.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+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.2020-01-03-191127L02-MK737-AB101.2x36mers.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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+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.2020-01-03-191127L03-MK842-AB101.2x36mers.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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+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.2020-01-03-191127L04-MK843-AB101.2x36mers.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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+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.2020-01-03-191127L05-MK844-AB101.2x36mers.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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+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.2020-01-03-191127L06-MK845-AB101.2x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+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.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+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.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+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.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+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.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+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.2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+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.2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+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.2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+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.2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+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.2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+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.2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+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.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+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.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+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.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+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.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+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.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+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.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+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.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+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.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+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.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+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.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+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.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+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.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+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.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+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.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+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.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+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.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+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.2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+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.2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+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.2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+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.2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+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.2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+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.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+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.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+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.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+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.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+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.2020-01-03-191103L01-MS521-AB101.2x36mers.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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+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.2020-01-03-191103L02-MS522-AB101.2x36mers.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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+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.2020-01-03-191103L03-MS523-AB101.2x36mers.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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+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.2020-01-03-191103L04-MS524-AB101.2x36mers.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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+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.2020-01-03-191103L05-MS527-AB101.2x36mers.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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+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.2020-01-03-191103L06-MS528-AB101.2x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+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.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+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.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+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.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+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.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+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.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+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.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+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.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+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.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+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.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+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.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+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.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+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.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+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.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+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.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+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.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+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.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+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.2020-01-03-191127L02-MK737-AB101.2x36mers.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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+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.2020-01-03-191127L03-MK842-AB101.2x36mers.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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+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.2020-01-03-191127L04-MK843-AB101.2x36mers.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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+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.2020-01-03-191127L05-MK844-AB101.2x36mers.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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+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.2020-01-03-191127L06-MK845-AB101.2x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+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.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+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.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+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.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+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.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+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.2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+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.2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+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.2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+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.2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+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.2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+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.2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+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.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+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.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+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.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+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.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+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.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+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.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+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.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+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.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+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.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+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.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+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.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+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.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+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.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+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.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+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.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+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.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+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.2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+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.2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+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.2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+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.2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+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.2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+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.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+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.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+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.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+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.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+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.2020-01-03-191103L01-MS521-AB101.2x36mers.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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+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.2020-01-03-191103L02-MS522-AB101.2x36mers.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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+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.2020-01-03-191103L03-MS523-AB101.2x36mers.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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+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.2020-01-03-191103L04-MS524-AB101.2x36mers.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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+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.2020-01-03-191103L05-MS527-AB101.2x36mers.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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+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.2020-01-03-191103L06-MS528-AB101.2x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+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.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+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.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+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.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+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.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+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.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+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.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+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.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+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.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+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.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+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.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+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.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+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.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+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.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+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.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+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.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+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.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+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.2020-01-03-191127L02-MK737-AB101.2x36mers.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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+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.2020-01-03-191127L03-MK842-AB101.2x36mers.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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+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.2020-01-03-191127L04-MK843-AB101.2x36mers.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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+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.2020-01-03-191127L05-MK844-AB101.2x36mers.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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+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.2020-01-03-191127L06-MK845-AB101.2x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+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.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+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.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+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.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+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.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+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.2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+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.2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+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.2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+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.2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+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.2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+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.2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+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.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+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.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+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.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+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.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+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.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+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.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+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.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+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.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+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.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+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.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+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.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+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.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+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.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+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.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+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.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+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.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+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.2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+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.2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+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.2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+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.2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+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.2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+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.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+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.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+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.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+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.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+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.2020-01-03-191103L01-MS521-AB101.2x36mers.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 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+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.2020-01-03-191103L02-MS522-AB101.2x36mers.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 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+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.2020-01-03-191103L03-MS523-AB101.2x36mers.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 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+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.2020-01-03-191103L04-MS524-AB101.2x36mers.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 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+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.2020-01-03-191103L05-MS527-AB101.2x36mers.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 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+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.2020-01-03-191103L06-MS528-AB101.2x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+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.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+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.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+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.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+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.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+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.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+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.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+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.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+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.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+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.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+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.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+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.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+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.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+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.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+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.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+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.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+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.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.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 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+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.2020-01-03-191127L02-MK737-AB101.2x36mers.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 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+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.2020-01-03-191127L03-MK842-AB101.2x36mers.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 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+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.2020-01-03-191127L04-MK843-AB101.2x36mers.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 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+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.2020-01-03-191127L05-MK844-AB101.2x36mers.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 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+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.2020-01-03-191127L06-MK845-AB101.2x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+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.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+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.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+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.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+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.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.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 2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+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.2020-01-03-191103L01-MS521-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+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.2020-01-03-191103L02-MS522-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+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.2020-01-03-191103L03-MS523-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+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.2020-01-03-191103L04-MS524-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+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.2020-01-03-191103L05-MS527-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+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.2020-01-03-191103L06-MS528-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L01-JK034-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L02-JK035-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L03-JK037-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+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.2020-01-03-191118L04-JK039-RAPA-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L09-MS207-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L10-MS289-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+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.2020-01-03-191119L11-MS290-RAPA-000-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+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.2020-01-03-191119L12-MS290-RAPA-020-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+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.2020-01-03-191119L13-MS290-RAPA-040-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+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.2020-01-03-191119L14-MS290-RAPA-060-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+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.2020-01-03-191119L15-MS290-RAPA-080-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+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.2020-01-03-191119L16-MS290-RAPA-100-AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L17-MS207-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L18-MS289-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+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.2020-01-03-191119L19-MS290-RAPA-000-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+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.2020-01-03-191119L20-MS290-RAPA-020-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+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.2020-01-03-191119L21-MS290-RAPA-040-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+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.2020-01-03-191119L22-MS290-RAPA-060-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+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.2020-01-03-191119L23-MS290-RAPA-080-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+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.2020-01-03-191119L24-MS290-RAPA-100-AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L25-MS207-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L26-MS289-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+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.2020-01-03-191119L27-MS290-RAPA-000-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+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.2020-01-03-191119L28-MS290-RAPA-020-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+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.2020-01-03-191119L29-MS290-RAPA-040-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+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.2020-01-03-191119L30-MS290-RAPA-060-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+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.2020-01-03-191119L31-MS290-RAPA-080-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+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.2020-01-03-191119L32-MS290-RAPA-100-AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+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.2020-01-03-191127L01-MK544-alpha-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+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.2020-01-03-191127L02-MK737-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+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.2020-01-03-191127L03-MK842-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+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.2020-01-03-191127L04-MK843-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+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.2020-01-03-191127L05-MK844-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+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.2020-01-03-191127L06-MK845-AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+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.2020-01-03-191127L07-MK846-AB05-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+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.2020-01-03-191127L08-MK846-AB05-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+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.2020-01-03-191127L09-MK846-AB102-A_600.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+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.2020-01-03-191127L10-MK846-AB102-B_100.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L01-MS521-AB101.1x36mers.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 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L02-MS522-AB101.1x36mers.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 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L03-MS523-AB101.1x36mers.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 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L04-MS524-AB101.1x36mers.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 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L05-MS527-AB101.1x36mers.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 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L06-MS528-AB101.1x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.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 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L02-MK737-AB101.1x36mers.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 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L03-MK842-AB101.1x36mers.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 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L04-MK843-AB101.1x36mers.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 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L05-MK844-AB101.1x36mers.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 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L06-MK845-AB101.1x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.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 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L01-MS521-AB101.1x36mers.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 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L02-MS522-AB101.1x36mers.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 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L03-MS523-AB101.1x36mers.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 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L04-MS524-AB101.1x36mers.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 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L05-MS527-AB101.1x36mers.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 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L06-MS528-AB101.1x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.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 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L02-MK737-AB101.1x36mers.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 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L03-MK842-AB101.1x36mers.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 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L04-MK843-AB101.1x36mers.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 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L05-MK844-AB101.1x36mers.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 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L06-MK845-AB101.1x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.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 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -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 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L01-MS521-AB101.1x36mers.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 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L02-MS522-AB101.1x36mers.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 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L03-MS523-AB101.1x36mers.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 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L04-MS524-AB101.1x36mers.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 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L05-MS527-AB101.1x36mers.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 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L06-MS528-AB101.1x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.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 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L02-MK737-AB101.1x36mers.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 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L03-MK842-AB101.1x36mers.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 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L04-MK843-AB101.1x36mers.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 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L05-MK844-AB101.1x36mers.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 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L06-MK845-AB101.1x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.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 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L01-MS521-AB101.1x36mers.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 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L02-MS522-AB101.1x36mers.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 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L03-MS523-AB101.1x36mers.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 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L04-MS524-AB101.1x36mers.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 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L05-MS527-AB101.1x36mers.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 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L06-MS528-AB101.1x36mers.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 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.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 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.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 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.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 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.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 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.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 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.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 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.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 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.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 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.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 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.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 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.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 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.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 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.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 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.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 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.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 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.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 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.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 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.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 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.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 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.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 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.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 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.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 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.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 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.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 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.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 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.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 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.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 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.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 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.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 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.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 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.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 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L02-MK737-AB101.1x36mers.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 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L03-MK842-AB101.1x36mers.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 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L04-MK843-AB101.1x36mers.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 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L05-MK844-AB101.1x36mers.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 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L06-MK845-AB101.1x36mers.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 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.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 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.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 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.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 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.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 2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L01-MS521-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L02-MS522-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L03-MS523-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L04-MS524-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L05-MS527-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_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.2020-01-03-191103L06-MS528-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L01-JK034-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L02-JK035-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L03-JK037-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_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.2020-01-03-191118L04-JK039-RAPA-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L01-MS207-RAPA-060-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.2020-01-03-191119L01-MS207-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L02-MS289-RAPA-060-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.2020-01-03-191119L02-MS289-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L03-MS290-RAPA-000-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.2020-01-03-191119L03-MS290-RAPA-000-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L04-MS290-RAPA-020-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.2020-01-03-191119L04-MS290-RAPA-020-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L05-MS290-RAPA-040-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.2020-01-03-191119L05-MS290-RAPA-040-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L06-MS290-RAPA-060-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.2020-01-03-191119L06-MS290-RAPA-060-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L07-MS290-RAPA-080-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.2020-01-03-191119L07-MS290-RAPA-080-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L08-MS290-RAPA-100-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.2020-01-03-191119L08-MS290-RAPA-100-input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L09-MS207-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L10-MS289-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L11-MS290-RAPA-000-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L12-MS290-RAPA-020-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L13-MS290-RAPA-040-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L14-MS290-RAPA-060-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L15-MS290-RAPA-080-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_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.2020-01-03-191119L16-MS290-RAPA-100-AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L17-MS207-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L18-MS289-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L19-MS290-RAPA-000-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L20-MS290-RAPA-020-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L21-MS290-RAPA-040-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L22-MS290-RAPA-060-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L23-MS290-RAPA-080-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_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.2020-01-03-191119L24-MS290-RAPA-100-AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L25-MS207-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L26-MS289-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L27-MS290-RAPA-000-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L28-MS290-RAPA-020-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L29-MS290-RAPA-040-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L30-MS290-RAPA-060-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L31-MS290-RAPA-080-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_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.2020-01-03-191119L32-MS290-RAPA-100-AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L01-MK544-alpha-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L02-MK737-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L03-MK842-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L04-MK843-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L05-MK844-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_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.2020-01-03-191127L06-MK845-AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L07-MK846-AB05-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L08-MK846-AB05-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_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.2020-01-03-191127L09-MK846-AB102-A_600.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_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.2020-01-03-191127L10-MK846-AB102-B_100.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes