python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL177_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL178_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL179_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL180_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL181_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T107_b12_Lung_PCW17.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T107_b12_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 - SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T132_b12_lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T132_b12_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 - SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T164_b12_Lung_PCW10.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T164_b12_Lung_PCW10.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 - SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T226_b12_Lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T226_b12_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 - SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T256_b12_Lung_PCW18.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T256_b12_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 - SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T286_b12_Lung_PCW14.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T286_b12_Lung_PCW14.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 - SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T304_b12_Lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T304_b12_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 - SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T408L_b12_Lung_PCW19.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T408L_b12_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 - SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL123_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL124_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL125_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL126_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL127_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL128_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL177_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL178_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL179_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL180_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.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 - SL181_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL177_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL177_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL178_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL178_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL179_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL179_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL180_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL180_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL181_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_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 - SL181_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T107_b12_Lung_PCW17.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T107_b12_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 - SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T132_b12_lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T132_b12_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 - SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T164_b12_Lung_PCW10.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T164_b12_Lung_PCW10.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 - SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T226_b12_Lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T226_b12_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 - SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T256_b12_Lung_PCW18.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T256_b12_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 - SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T286_b12_Lung_PCW14.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T286_b12_Lung_PCW14.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 - SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T304_b12_Lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T304_b12_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 - SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T408L_b12_Lung_PCW19.end1.fastq.gz SL159_b12_ATAC_LungRedo.barcodes_annotated.barcode_T408L_b12_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 - SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_PCW21.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T238_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_PCW18.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T269_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL123_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL124_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL125_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL126_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL127_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_PCW21.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T303_b10_Esophagus_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 - SL128_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_PCW21.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T322_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_PCW17.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T35_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_PCW17.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T399_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL122_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL123_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL123_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL124_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL124_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL125_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL125_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL126_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL126_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL127_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL127_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_PCW20.end1.fastq.gz SL128_b10_ATAC_StomachEsophagus.barcodes_annotated.barcode_T53_b10_Stomach_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 - SL128_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique