python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-13189-1/A-13189-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-13189-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-13189-2/A-13189-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-13189-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-13190-1/A-13190-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-13190-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-13190-2/A-13190-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-13190-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-15171-1/A-15171-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-15171-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-15171-2/A-15171-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-15171-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-15173-1/A-15173-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-15173-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-15173-2/A-15173-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-15173-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-N4293-1/A-N4293-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-N4293-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-N4293-2/A-N4293-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-N4293-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-N4371-1/A-N4371-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-N4371-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/A-N4371-2/A-N4371-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.A-N4371-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/KO-13004-1/KO-13004-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.KO-13004-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/KO-13004-2/KO-13004-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.KO-13004-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/KO-13006-1/KO-13006-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.KO-13006-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/KO-13006-2/KO-13006-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.KO-13006-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/KO-N4293-1/KO-N4293-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.KO-N4293-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/KO-N4293-2/KO-N4293-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.KO-N4293-2.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/KO-N4371-1/KO-N4371-1.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.KO-N4371-1.RPM -RPM -uniqueBAM
python ~/code/bedRPKMfromBAM.py A-N4371.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.indRep.IDR-0.05.gz 0 /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-ATAC/KO-N4371-2/KO-N4371-2.2x75mers-trimmed.bwa-mem.hg19-female.nochrM.dedup.bam ~/genomes/hg19/hg19.chrom.sizes A-N4371.indRep.IDR-0.05.KO-N4371-2.RPM -RPM -uniqueBAM