python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.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 SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.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 SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.chrM.bam SAMstats-SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.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 SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.chrM.bam SAMstats-SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.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 SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.chrM.bam SAMstats-SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.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 SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.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 SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.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 SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.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 SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.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 SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM.bam SAMstats-SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.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 SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.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 SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.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 SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM.bam SAMstats-SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.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 SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.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 SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.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 SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.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 SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.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 SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.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 SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.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 SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.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 SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.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 SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.chrM.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.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 SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.bam SAMstats-SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.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/SAMstats.py SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.bam SAMstats-SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.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/SAMstats.py SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.bam SAMstats-SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.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/SAMstats.py SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.bam SAMstats-SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.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/SAMstats.py SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.bam SAMstats-SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.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/SAMstats.py SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.bam SAMstats-SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.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/SAMstats.py SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.bam SAMstats-SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.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/SAMstats.py SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.bam SAMstats-SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.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/SAMstats.py SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.bam SAMstats-SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.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/SAMstats.py SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.bam SAMstats-SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.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/SAMstats.py SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.bam SAMstats-SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.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/SAMstats.py SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.bam SAMstats-SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.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/SAMstats.py SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.bam SAMstats-SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.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/SAMstats.py SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.bam SAMstats-SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.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/SAMstats.py SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.bam SAMstats-SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.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/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.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/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.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/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.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/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.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/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.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/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.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/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.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 SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.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 SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.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 SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.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 SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.chrM.bam SAMstats-SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.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 SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.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 SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.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 SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.chrM.bam SAMstats-SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.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 SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.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 SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.bam SAMstats-SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.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/SAMstats.py SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.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/SAMstats.py SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.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/SAMstats.py SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.bam SAMstats-SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.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/SAMstats.py SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.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/SAMstats.py SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.bam SAMstats-SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.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/SAMstats.py SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.bam SAMstats-SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.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/SAMstats.py SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.bam SAMstats-SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.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 SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.BC_dedup.bam -addBC &