python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM-excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L12_exp260316_RPE1_t90h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L01_exp260401_RPE1toS2_2to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L02_exp260401_RPE1toS2_6to1_1_kit_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L04_exp260401_RPE1toS2_6to1_2_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L05_exp260401_RPE1toS2_2to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L06_exp260401_RPE1toS2_6to1_3_trizol_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L07_exp260401_RPE1toS2_2to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260410L08_exp260401_RPE1toS2_6to1_3_kit_gDNA.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L01_exp260316_RPE1_INPUT_t18h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L02_exp260316_RPE1_INPUT_t43h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L03_exp260316_RPE1_INPUT_t90h.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 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L04_exp260316_RPE1_t18h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L05_exp260316_RPE1_t43h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-500bp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-500bp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-500bp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.TSS-2kbp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes TSS-2kbp.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.Drosophila_melanogaster.BDGP6.90.fixed.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/dm6.nochrM.chrom.sizes genes-500bp-1kbp-ext.dm6.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.genes-500bp-1kbp-ext 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes genes-500bp-1kbp-ext.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L06_exp260316_RPE1_t90h_CTD-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L07_exp260316_RPE1_t18h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L08_exp260316_RPE1_t43h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L09_exp260316_RPE1_t90h_S5P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L10_exp260316_RPE1_t18h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.midPoint.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPKM -uniqueBAM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.2016-11-16-refFlat.TSS-2kbp.bed 0 2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.hg38+dm6.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38+dm6/hg38.nochrM.chrom.sizes TSS-2kbp.hg38.2026-04-24-MS260403L11_exp260316_RPE1_t43h_S2P-ChIP.2x75mers.nochrM.ERMTOC.RPM -RPM -uniqueBAM -excludeReadsMappingToOtherChromosomes