python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.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 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L01_exp260204_MS8_SCD_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.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 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L02_exp260204_MS8_SCD_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.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 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L03_exp260204_MS8_SCD_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.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 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L04_exp260204_MS8_SCD_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.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 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L05_exp260204_MS8_SCGE_no-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.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 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L06_exp260204_MS8_SCGE_05min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.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 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L07_exp260204_MS8_SCGE_10min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.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 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2026-02-25-LHG260210L08_exp260204_MS8_SCGE_20min-EU.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint