python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L01-exp250721_RPE1_ChIP_1_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L02-exp250721_RPE1_ChIP_1_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L03-exp250721_RPE1_ChIP_2_DMSO_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L04-exp250721_RPE1_ChIP_2_TPL_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L05-exp250721_RPE1_ChIP_1_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L06-exp250721_RPE1_ChIP_1_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L07-exp250721_RPE1_ChIP_2_DMSO_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L08-exp250721_RPE1_ChIP_2_TPL_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L09-exp250721_RPE1_ChIP_1_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L10-exp250721_RPE1_ChIP_1_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L11-exp250721_RPE1_ChIP_2_DMSO_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250827L12-exp250721_RPE1_ChIP_2_TPL_Beads.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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-2kbp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.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-500bp-1kbp-ext 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L13-exp250728_RPE1_ChIP_Palbo-18h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L14-exp250728_RPE1_ChIP_Palbo-48h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L15-exp250728_RPE1_ChIP_Palbo-96h_INPUT.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L16-exp250728_RPE1_ChIP_Palbo-18h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L17-exp250728_RPE1_ChIP_Palbo-48h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2025-09-16-MS250902L18-exp250728_RPE1_ChIP_Palbo-96h_ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes