python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T40_b16_Adr_PCW17.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T40_b16_Adr_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T40_b16_Adr_PCW17.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T40_b16_Adr_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T390_b16_Adr_PCW13.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T390_b16_Adr_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T390_b16_Adr_PCW13.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T390_b16_Adr_PCW13.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T318_b16_Adr_PCW21.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T318_b16_Adr_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T318_b16_Adr_PCW21.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T318_b16_Adr_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T314_b16_Spleen_PCW21.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T314_b16_Spleen_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T314_b16_Spleen_PCW21.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T314_b16_Spleen_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T273_b16_Adr_PCW18.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T273_b16_Adr_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T273_b16_Adr_PCW18.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T273_b16_Adr_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T176_b16_Thyroid_PCW19.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T176_b16_Thyroid_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T176_b16_Thyroid_PCW19.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T176_b16_Thyroid_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T136_b16_Thyroid_PCW21.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T136_b16_Thyroid_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T136_b16_Thyroid_PCW21.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T136_b16_Thyroid_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T40_b16_Adr_PCW17.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T40_b16_Adr_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T40_b16_Adr_PCW17.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T40_b16_Adr_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T390_b16_Adr_PCW13.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T390_b16_Adr_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T390_b16_Adr_PCW13.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T390_b16_Adr_PCW13.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T318_b16_Adr_PCW21.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T318_b16_Adr_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T318_b16_Adr_PCW21.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T318_b16_Adr_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T314_b16_Spleen_PCW21.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T314_b16_Spleen_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T314_b16_Spleen_PCW21.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T314_b16_Spleen_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T273_b16_Adr_PCW18.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T273_b16_Adr_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T273_b16_Adr_PCW18.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T273_b16_Adr_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T176_b16_Thyroid_PCW19.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T176_b16_Thyroid_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T176_b16_Thyroid_PCW19.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T176_b16_Thyroid_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL261_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T136_b16_Thyroid_PCW21.end1.fastq.gz SL261_b15_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 - SL261_b15_ATAC_AdrenalThyroidSpleen.T136_b16_Thyroid_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL262_b15_ATAC_AdrenalThyroidSpleen.barcodes_annotated.barcode_T136_b16_Thyroid_PCW21.end1.fastq.gz SL262_b15_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_b15_ATAC_AdrenalThyroidSpleen.T136_b16_Thyroid_PCW21.2x36mers.hg38.unique