python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py BMMC_single_donor_ATAC.2x36mers.hg38.chrM.bam SAMstats-BMMC_single_donor_ATAC.2x36mers.hg38.chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py BMMC_single_donor_ATAC.2x36mers.hg38.unique.bam SAMstats-BMMC_single_donor_ATAC.2x36mers.hg38.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BMMC_single_donor_ATAC.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BMMC_single_donor_ATAC.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- BMMC_single_donor_ATAC.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BMMC_single_donor_ATAC.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py BMMC_single_donor_ATAC.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BMMC_single_donor_ATAC.2x36mers.hg38.unique.BC_dedup.bam -addBC &