python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL299_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL299_skin_atac_redo.T11_b19_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 SL299_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL299_skin_atac_redo.T45_b19_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 SL299_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.chrM.bam SAMstats-SL299_skin_atac_redo.T187_b19_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 SL299_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL299_skin_atac_redo.T299_b19_Scalp_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 SL299_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL299_skin_atac_redo.T408S_b19_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 SL300_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL300_skin_atac_redo.T11_b19_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 SL300_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL300_skin_atac_redo.T45_b19_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 SL300_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.chrM.bam SAMstats-SL300_skin_atac_redo.T187_b19_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 SL300_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL300_skin_atac_redo.T299_b19_Scalp_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 SL300_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL300_skin_atac_redo.T408S_b19_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 SL299_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL299_skin_atac_redo.T11_b19_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 SL299_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam SAMstats-SL299_skin_atac_redo.T45_b19_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 SL299_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam SAMstats-SL299_skin_atac_redo.T187_b19_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 SL299_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam SAMstats-SL299_skin_atac_redo.T299_b19_Scalp_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 SL299_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL299_skin_atac_redo.T408S_b19_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 SL300_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL300_skin_atac_redo.T11_b19_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 SL300_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam SAMstats-SL300_skin_atac_redo.T45_b19_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 SL300_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam SAMstats-SL300_skin_atac_redo.T187_b19_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 SL300_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam SAMstats-SL300_skin_atac_redo.T299_b19_Scalp_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 SL300_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL300_skin_atac_redo.T408S_b19_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/PEInsertDistFromBAM.py SL299_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL299_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL299_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL299_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL299_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL300_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL300_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL300_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL300_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL300_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL299_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL299_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL299_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL299_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL299_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL300_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL300_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL300_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL300_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL300_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL299_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T11_b19_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 SL299_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T45_b19_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 SL299_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T187_b19_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 SL299_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T299_b19_Scalp_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 SL299_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL299_skin_atac_redo.T408S_b19_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 SL300_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T11_b19_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 SL300_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T45_b19_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 SL300_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T187_b19_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 SL300_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T299_b19_Scalp_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 SL300_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL300_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL303_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL303_skin_atac_redo.T11_b19_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 SL303_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL303_skin_atac_redo.T45_b19_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 SL303_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.chrM.bam SAMstats-SL303_skin_atac_redo.T187_b19_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 SL303_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL303_skin_atac_redo.T299_b19_Scalp_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 SL303_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL303_skin_atac_redo.T408S_b19_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 SL304_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL304_skin_atac_redo.T11_b19_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 SL304_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL304_skin_atac_redo.T45_b19_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 SL304_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.chrM.bam SAMstats-SL304_skin_atac_redo.T187_b19_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 SL304_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL304_skin_atac_redo.T299_b19_Scalp_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 SL304_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL304_skin_atac_redo.T408S_b19_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 SL303_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL303_skin_atac_redo.T11_b19_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 SL303_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam SAMstats-SL303_skin_atac_redo.T45_b19_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 SL303_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam SAMstats-SL303_skin_atac_redo.T187_b19_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 SL303_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam SAMstats-SL303_skin_atac_redo.T299_b19_Scalp_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 SL303_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL303_skin_atac_redo.T408S_b19_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 SL304_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL304_skin_atac_redo.T11_b19_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 SL304_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam SAMstats-SL304_skin_atac_redo.T45_b19_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 SL304_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam SAMstats-SL304_skin_atac_redo.T187_b19_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 SL304_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam SAMstats-SL304_skin_atac_redo.T299_b19_Scalp_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 SL304_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL304_skin_atac_redo.T408S_b19_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/PEInsertDistFromBAM.py SL303_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL303_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL303_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL303_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL303_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL304_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL304_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL304_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL304_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL304_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL303_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL303_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL303_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL303_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL303_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL304_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL304_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL304_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL304_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL304_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL303_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T11_b19_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 SL303_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T45_b19_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 SL303_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T187_b19_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 SL303_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T299_b19_Scalp_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 SL303_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL303_skin_atac_redo.T408S_b19_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 SL304_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T11_b19_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 SL304_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T45_b19_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 SL304_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T187_b19_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 SL304_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T299_b19_Scalp_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 SL304_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL304_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL301_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL301_skin_atac_redo.T11_b19_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 SL301_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL301_skin_atac_redo.T45_b19_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 SL301_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.chrM.bam SAMstats-SL301_skin_atac_redo.T187_b19_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 SL301_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL301_skin_atac_redo.T299_b19_Scalp_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 SL301_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL301_skin_atac_redo.T408S_b19_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 SL302_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL302_skin_atac_redo.T11_b19_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 SL302_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL302_skin_atac_redo.T45_b19_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 SL302_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.chrM.bam SAMstats-SL302_skin_atac_redo.T187_b19_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 SL302_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL302_skin_atac_redo.T299_b19_Scalp_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 SL302_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL302_skin_atac_redo.T408S_b19_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 SL301_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL301_skin_atac_redo.T11_b19_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 SL301_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam SAMstats-SL301_skin_atac_redo.T45_b19_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 SL301_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam SAMstats-SL301_skin_atac_redo.T187_b19_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 SL301_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam SAMstats-SL301_skin_atac_redo.T299_b19_Scalp_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 SL301_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL301_skin_atac_redo.T408S_b19_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 SL302_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL302_skin_atac_redo.T11_b19_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 SL302_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam SAMstats-SL302_skin_atac_redo.T45_b19_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 SL302_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam SAMstats-SL302_skin_atac_redo.T187_b19_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 SL302_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam SAMstats-SL302_skin_atac_redo.T299_b19_Scalp_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 SL302_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam SAMstats-SL302_skin_atac_redo.T408S_b19_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/PEInsertDistFromBAM.py SL301_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL301_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL301_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL301_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL301_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL302_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL302_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL302_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL302_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL302_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL301_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL301_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL301_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL301_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL301_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL302_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL302_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL302_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL302_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL302_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL301_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T11_b19_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 SL301_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T45_b19_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 SL301_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T187_b19_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 SL301_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T299_b19_Scalp_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 SL301_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL301_skin_atac_redo.T408S_b19_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 SL302_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T11_b19_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 SL302_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T45_b19_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 SL302_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T187_b19_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 SL302_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T299_b19_Scalp_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 SL302_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL302_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &