python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L01_exp250704_RPE1_5:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L02_exp250704_RPE1_10:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L03_exp250704_RPE1_20:1-S2-ratio_INPUT.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L04_exp250704_RPE1_5:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L05_exp250704_RPE1_10:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-07-29-MS250708L06_exp250704_RPE1_20:1-S2-ratio_Rpb1-CTD-ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint