python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_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/PEInsertDistFromBAM.py SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T90_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T90_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_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/PEInsertDistFromBAM.py SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T165_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T233_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T23_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T270_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T314_b17_Spleen_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 SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T406_b17_Thymus_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 SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL242_b17_ATAC_SpleenThymus.T88_b17_Spleen_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 SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL243_b17_ATAC_SpleenThymus.T88_b17_Spleen_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 SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL244_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique.BC_dedup.bam -addBC &