python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.chrM.bam SAMstats-BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.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 BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.chrM.bam SAMstats-BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.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 BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.chrM.bam SAMstats-BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.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 BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.chrM.bam SAMstats-BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.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 BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.unique.bam SAMstats-BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.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 BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.unique.bam SAMstats-BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.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 BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.unique.bam SAMstats-BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.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 BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.unique.bam SAMstats-BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.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 BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM.py --- BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM.py --- BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM.py --- BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM.py --- BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.unique.BC_dedup.bam -addBC &