python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L01_exp251028_RPE1_ChIP_1_INPUT_DMSO.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L02_exp251028_RPE1_ChIP_1_INPUT_TPL.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L03_exp251111_RPE1_ChIP_2_INPUT_DMSO.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L04_exp251111_RPE1_ChIP_2_INPUT_TPL.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L05_exp251028_RPE1_ChIP_1_ChIP_RNAPII_DMSO.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L06_exp251028_RPE1_ChIP_1_ChIP_RNAPII_TPL.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L07_exp251028_RPE1_ChIP_1_ChIP_S2P_DMSO.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L08_exp251028_RPE1_ChIP_1_ChIP_S2P_TPL.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L09_exp251111_RPE1_ChIP_2_ChIP_S2P_DMSO.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L10_exp251111_RPE1_ChIP_2_ChIP_S2P_TPL.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L11_exp251111_RPE1_ChIP_2_ChIP_S5P_DMSO.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.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 2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-01-03-MS251125L12_exp251111_RPE1_ChIP_2_ChIP_S5P_TPL.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes