python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL283_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL283_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL283_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL284_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL284_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL284_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL285_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL285_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL285_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL286_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL286_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL286_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL288_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL288_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL288_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL287_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL287_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL287_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique