python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.sacCer3.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.sacCer3.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200224L79_exp200120_MS208_RAPA100_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.2020-03-16-200224L79_exp200120_MS208_RAPA100_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 2020-03-16-200224L80_exp200120_MS208_RAPAON_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.2020-03-16-200224L80_exp200120_MS208_RAPAON_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.sacCer3.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.sacCer3.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.sacCer3.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.sacCer3.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.sacCer3.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.sacCer3.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.sacCer3.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.sacCer3.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.sacCer3.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.sacCer3.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.sacCer3.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.sacCer3.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.sacCer3.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.sacCer3.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.sacCer3.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.sacCer3.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.sacCer3.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.sacCer3.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.sacCer3.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.sacCer3.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.sacCer3.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.sacCer3.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.sacCer3.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.sacCer3.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.sacCer3.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.sacCer3.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.sacCer3.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.sacCer3.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.sacCer3.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.sacCer3.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.sacCer3.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.sacCer3.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.sacCer3.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.sacCer3.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.sacCer3.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.sacCer3.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.sacCer3.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.sacCer3.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.sacCer3.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.sacCer3.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.sacCer3.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.sacCer3.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.sacCer3.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.sacCer3.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.sacCer3.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.sacCer3.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.sacCer3.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_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 2020-03-16-200216L01_MS207_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.2020-03-16-200216L01_MS207_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 2020-03-16-200216L02_MS289_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.2020-03-16-200216L02_MS289_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 2020-03-16-200216L03_MS281_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.2020-03-16-200216L03_MS281_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 2020-03-16-200216L04_MS283_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.2020-03-16-200216L04_MS283_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 2020-03-16-200216L05_MS285_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.2020-03-16-200216L05_MS285_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 2020-03-16-200216L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L06_MS287_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 2020-03-16-200216L07_MS207_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.2020-03-16-200216L07_MS207_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 2020-03-16-200216L08_MS289_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.2020-03-16-200216L08_MS289_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 2020-03-16-200216L09_MS282_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.2020-03-16-200216L09_MS282_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 2020-03-16-200216L10_MS284_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.2020-03-16-200216L10_MS284_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 2020-03-16-200216L11_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L11_MS286_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 2020-03-16-200216L12_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200216L12_MS288_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 2020-03-16-200216L13_MS207_RAPA_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.2020-03-16-200216L13_MS207_RAPA_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 2020-03-16-200216L14_MS289_RAPA_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.2020-03-16-200216L14_MS289_RAPA_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 2020-03-16-200216L87_MS208_DMSO_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.2020-03-16-200216L87_MS208_DMSO_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 2020-03-16-200216L88_MS208_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.2020-03-16-200216L88_MS208_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 2020-03-16-200216L89_MS208_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.2020-03-16-200216L89_MS208_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 2020-03-16-200216L18_MS208_RAPA-ON_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.2020-03-16-200216L18_MS208_RAPA-ON_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 2020-03-16-200216L15_MS208_DMSO_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.2020-03-16-200216L15_MS208_DMSO_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 2020-03-16-200216L17_MS208_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.2020-03-16-200216L17_MS208_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 2020-03-16-200216L25_MS207_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.2020-03-16-200216L25_MS207_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 2020-03-16-200216L26_MS289_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.2020-03-16-200216L26_MS289_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 2020-03-16-200216L27_MS281_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.2020-03-16-200216L27_MS281_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 2020-03-16-200216L28_MS283_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.2020-03-16-200216L28_MS283_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 2020-03-16-200216L29_MS285_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.2020-03-16-200216L29_MS285_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 2020-03-16-200216L30_MS287_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.2020-03-16-200216L30_MS287_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 2020-03-16-200216L31_MS207_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.2020-03-16-200216L31_MS207_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 2020-03-16-200216L32_MS289_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.2020-03-16-200216L32_MS289_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 2020-03-16-200216L33_MS282_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.2020-03-16-200216L33_MS282_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 2020-03-16-200216L33_MS284_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.2020-03-16-200216L33_MS284_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 2020-03-16-200216L35_MS286_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.2020-03-16-200216L35_MS286_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 2020-03-16-200216L36_MS288_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.2020-03-16-200216L36_MS288_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 2020-03-16-200216L37_MS207_RAPA_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.2020-03-16-200216L37_MS207_RAPA_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 2020-03-16-200216L38_MS289_RAPA_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.2020-03-16-200216L38_MS289_RAPA_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 2020-03-16-200216L39_MS208_DMSO_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.2020-03-16-200216L39_MS208_DMSO_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 2020-03-16-200216L40_MS208_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.2020-03-16-200216L40_MS208_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 2020-03-16-200216L41_MS208_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.2020-03-16-200216L41_MS208_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 2020-03-16-200216L42_MS208_RAPA-ON_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.2020-03-16-200216L42_MS208_RAPA-ON_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 2020-03-16-200224L63_exp200101_MS207_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.2020-03-16-200224L63_exp200101_MS207_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 2020-03-16-200224L64_exp200101_MS289_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.2020-03-16-200224L64_exp200101_MS289_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 2020-03-16-200224L65_exp200101_MS281_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.2020-03-16-200224L65_exp200101_MS281_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 2020-03-16-200224L66_exp200101_MS283_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.2020-03-16-200224L66_exp200101_MS283_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 2020-03-16-200224L67_exp200101_MS285_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.2020-03-16-200224L67_exp200101_MS285_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 2020-03-16-200224L68_exp200101_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L68_exp200101_MS287_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 2020-03-16-200224L69_exp200101_MS207_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.2020-03-16-200224L69_exp200101_MS207_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 2020-03-16-200224L70_exp200101_MS289_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.2020-03-16-200224L70_exp200101_MS289_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 2020-03-16-200224L71_exp200101_MS282_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.2020-03-16-200224L71_exp200101_MS282_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 2020-03-16-200224L72_exp200101_MS284_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.2020-03-16-200224L72_exp200101_MS284_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 2020-03-16-200224L73_exp200101_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L73_exp200101_MS286_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 2020-03-16-200224L74_exp200101_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2020-03-16-200224L74_exp200101_MS288_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 2020-03-16-200224L75_exp200120_MS207_RAPA100_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.2020-03-16-200224L75_exp200120_MS207_RAPA100_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 2020-03-16-200224L76_exp200120_MS289_RAPA065_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.2020-03-16-200224L76_exp200120_MS289_RAPA065_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 2020-03-16-200224L77_exp200120_MS208_DMSO100_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.2020-03-16-200224L77_exp200120_MS208_DMSO100_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 2020-03-16-200224L78_exp200120_MS208_RAPA040_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.2020-03-16-200224L78_exp200120_MS208_RAPA040_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -RPKM -excludeReadsMappingToOtherChromosomes