python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T233_b17_Thymus_PCW21.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T233_b17_Thymus_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 - SL230_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T23_b17_Thymus_PCW17.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T23_b17_Thymus_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 - SL230_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T270_b17_Spleen_PCW18.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T270_b17_Spleen_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 - SL230_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T314_b17_Spleen_PCW21.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T314_b17_Spleen_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 - SL230_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T406_b17_Thymus_PCW19.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T406_b17_Thymus_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 - SL230_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T88_b17_Spleen_PCW18.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T88_b17_Spleen_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 - SL230_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T90_b17_Thymus_PCW18.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T90_b17_Thymus_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 - SL230_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T165_b17_Spleen_PCW19.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T165_b17_Spleen_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 - SL230_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T176_b16_Thyroid_PCW19.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T176_b16_Thyroid_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T176_b16_Thyroid_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T273_b16_Adr_PCW18.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T273_b16_Adr_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T273_b16_Adr_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T314_b16_Spleen_PCW21.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T314_b16_Spleen_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T314_b16_Spleen_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T318_b16_Adr_PCW21.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T318_b16_Adr_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T318_b16_Adr_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T390_b16_Adr_PCW13.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T390_b16_Adr_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T390_b16_Adr_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T40_b16_Adr_PCW17.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T40_b16_Adr_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T40_b16_Adr_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T136_b16_Thyroid_PCW21.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T136_b16_Thyroid_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T136_b16_Thyroid_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T235_b15_Liver_PCW21.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T235_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T235_b15_Liver_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T275_b15_Liver_PCW18.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T275_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T275_b15_Liver_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T350_b15_Liver_PCW21.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T350_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T350_b15_Liver_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T375_b15_Liver_PCW15.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T375_b15_Liver_PCW15.end2.fastq.gz -trim 36 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 - SL211_b15_ATAC_LiverRedo.T375_b15_Liver_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T398_b15_Liver_PCW17.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T398_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T398_b15_Liver_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T71_b15_Liver_PCW18.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T71_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T71_b15_Liver_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T166_b15_Liver_PCW19.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T166_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T166_b15_Liver_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T11_b14_Skin_PCW19.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T11_b14_Skin_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 - SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T178_b14_Skin_PCW19.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T178_b14_Skin_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 - SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T187_b14_Skin_PCW23.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T187_b14_Skin_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 - SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T408S_b14_Skin_PCW19.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T408S_b14_Skin_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 - SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T45_b14_Skin_PCW17.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T45_b14_Skin_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 - SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T60_b14_Skin_PCW20.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T60_b14_Skin_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 - SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T85_b14_Skin_PCW18.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T85_b14_Skin_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 - SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T109_b14_Skin_PCW17.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T109_b14_Skin_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 - SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.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 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 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 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 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 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 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 SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T123_b9_Muscle_PCW22.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T123_b9_Muscle_PCW22.end2.fastq.gz -trim 36 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 - SL118_b9_ATAC_muscle.T123_b9_Muscle_PCW22.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T161_b9_Muscle_PCW10.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T161_b9_Muscle_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 - SL118_b9_ATAC_muscle.T161_b9_Muscle_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T377_b9_Muscle_PCW15.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T377_b9_Muscle_PCW15.end2.fastq.gz -trim 36 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 - SL118_b9_ATAC_muscle.T377_b9_Muscle_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T44_b9_Muscle_PCW17.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T44_b9_Muscle_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 - SL118_b9_ATAC_muscle.T44_b9_Muscle_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T61_b9_Muscle_PCW20.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T61_b9_Muscle_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 - SL118_b9_ATAC_muscle.T61_b9_Muscle_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T87_b9_Muscle_PCW18.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T87_b9_Muscle_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 - SL118_b9_ATAC_muscle.T87_b9_Muscle_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T96_b9_Muscle_PCW17.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T96_b9_Muscle_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 - SL118_b9_ATAC_muscle.T96_b9_Muscle_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T10_b9_Muscle_PCW19.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T10_b9_Muscle_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 - SL118_b9_ATAC_muscle.T10_b9_Muscle_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T233_b17_Thymus_PCW21.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T233_b17_Thymus_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 - SL230_b17_ATAC_SpleenThymus.T233_b17_Thymus_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T23_b17_Thymus_PCW17.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T23_b17_Thymus_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 - SL230_b17_ATAC_SpleenThymus.T23_b17_Thymus_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T270_b17_Spleen_PCW18.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T270_b17_Spleen_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 - SL230_b17_ATAC_SpleenThymus.T270_b17_Spleen_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T314_b17_Spleen_PCW21.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T314_b17_Spleen_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 - SL230_b17_ATAC_SpleenThymus.T314_b17_Spleen_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T406_b17_Thymus_PCW19.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T406_b17_Thymus_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 - SL230_b17_ATAC_SpleenThymus.T406_b17_Thymus_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T88_b17_Spleen_PCW18.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T88_b17_Spleen_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 - SL230_b17_ATAC_SpleenThymus.T88_b17_Spleen_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T90_b17_Thymus_PCW18.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T90_b17_Thymus_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 - SL230_b17_ATAC_SpleenThymus.T90_b17_Thymus_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T165_b17_Spleen_PCW19.end1.fastq.gz SL230_b17_ATAC_SpleenThymus.barcodes_annotated.barcode_T165_b17_Spleen_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 - SL230_b17_ATAC_SpleenThymus.T165_b17_Spleen_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T176_b16_Thyroid_PCW19.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T176_b16_Thyroid_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T176_b16_Thyroid_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T273_b16_Adr_PCW18.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T273_b16_Adr_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T273_b16_Adr_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T314_b16_Spleen_PCW21.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T314_b16_Spleen_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T314_b16_Spleen_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T318_b16_Adr_PCW21.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T318_b16_Adr_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T318_b16_Adr_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T390_b16_Adr_PCW13.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T390_b16_Adr_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T390_b16_Adr_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T40_b16_Adr_PCW17.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T40_b16_Adr_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T40_b16_Adr_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T136_b16_Thyroid_PCW21.end1.fastq.gz SL262_b16_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T136_b16_Thyroid_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 - SL262_b16_ATAC_AdrenalThyroidSpleen.T136_b16_Thyroid_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T235_b15_Liver_PCW21.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T235_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T235_b15_Liver_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T275_b15_Liver_PCW18.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T275_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T275_b15_Liver_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T350_b15_Liver_PCW21.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T350_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T350_b15_Liver_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T375_b15_Liver_PCW15.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T375_b15_Liver_PCW15.end2.fastq.gz -trim 36 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 - SL211_b15_ATAC_LiverRedo.T375_b15_Liver_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T398_b15_Liver_PCW17.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T398_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T398_b15_Liver_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T71_b15_Liver_PCW18.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T71_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T71_b15_Liver_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T166_b15_Liver_PCW19.end1.fastq.gz SL211_b15_ATAC_LiverRedo.barcodes_annotated.barcode_T166_b15_Liver_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 - SL211_b15_ATAC_LiverRedo.T166_b15_Liver_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T11_b14_Skin_PCW19.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T11_b14_Skin_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 - SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T178_b14_Skin_PCW19.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T178_b14_Skin_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 - SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T187_b14_Skin_PCW23.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T187_b14_Skin_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 - SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T408S_b14_Skin_PCW19.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T408S_b14_Skin_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 - SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T45_b14_Skin_PCW17.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T45_b14_Skin_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 - SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T60_b14_Skin_PCW20.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T60_b14_Skin_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 - SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T85_b14_Skin_PCW18.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T85_b14_Skin_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 - SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T109_b14_Skin_PCW17.end1.fastq.gz SL187_b14_ATAC_Skin.barcodes_annotated.barcode_T109_b14_Skin_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 - SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T180_b13_Eye_PCW19.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T186_b13_Eye_PCW23.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T410_b13_Eye_PCW13.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T51_b13_Eye_PCW20.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T5_b13_Eye_PCW19.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T79_b13_Eye_PCW18.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL182_b13_ATAC_EyeRedo.barcodes_annotated.barcode_T106_b13_Eye_PCW17.end1.fastq.gz SL182_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 - SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.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 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 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 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 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 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 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 SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T123_b9_Muscle_PCW22.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T123_b9_Muscle_PCW22.end2.fastq.gz -trim 36 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 - SL118_b9_ATAC_muscle.T123_b9_Muscle_PCW22.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T161_b9_Muscle_PCW10.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T161_b9_Muscle_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 - SL118_b9_ATAC_muscle.T161_b9_Muscle_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T377_b9_Muscle_PCW15.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T377_b9_Muscle_PCW15.end2.fastq.gz -trim 36 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 - SL118_b9_ATAC_muscle.T377_b9_Muscle_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T44_b9_Muscle_PCW17.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T44_b9_Muscle_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 - SL118_b9_ATAC_muscle.T44_b9_Muscle_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T61_b9_Muscle_PCW20.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T61_b9_Muscle_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 - SL118_b9_ATAC_muscle.T61_b9_Muscle_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T87_b9_Muscle_PCW18.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T87_b9_Muscle_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 - SL118_b9_ATAC_muscle.T87_b9_Muscle_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T96_b9_Muscle_PCW17.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T96_b9_Muscle_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 - SL118_b9_ATAC_muscle.T96_b9_Muscle_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T10_b9_Muscle_PCW19.end1.fastq.gz SL118_b9_ATAC_muscle.barcodes_annotated.barcode_T10_b9_Muscle_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 - SL118_b9_ATAC_muscle.T10_b9_Muscle_PCW19.2x36mers.hg38.unique