python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_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 SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_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 SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_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 SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.chrM.bam SAMstats-SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_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 SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.bam SAMstats-SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_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 SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.bam SAMstats-SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_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 SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.bam SAMstats-SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_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 SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.bam SAMstats-SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_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 SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_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 SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL337_b22_ATAC_thyroidredo.T136_b22_Thyroid_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 SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL337_b22_ATAC_thyroidredo.T176_b22_Thyroid_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 SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL338_b22_ATAC_thyroidredo.T136_b22_Thyroid_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 SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL338_b22_ATAC_thyroidredo.T176_b22_Thyroid_PCW19.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.chrM.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.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 SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.chrM.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.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 SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.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 SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.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 SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T373_b21_Kidney_PCW15.2x36mers.hg38.unique.BC_dedup.bam -addBC &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.chrM.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.chrM.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.chrM.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.bam SAMstats-SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.bam SAMstats-SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_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/PEInsertDistFromBAM.py SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_dedup-V2.py SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T108_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T271_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T228_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T42_b21_Kidney_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 SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL329_b21_ATAC_kidneyreredo.T397_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T108_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_PCW18.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T271_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_PCW21.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T228_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T42_b21_Kidney_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 SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes SL330_b21_ATAC_kidneyreredo.T397_b21_Kidney_PCW17.2x36mers.hg38.unique.BC_dedup.bam -addBC &