python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T11_b19_Skin_PCW19.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T11_b19_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 - SL297_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T187_b19_Skin_PCW23.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T187_b19_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 - SL297_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T299_b19_Scalp_PCW21.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T299_b19_Scalp_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 - SL297_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T408S_b19_Skin_PCW19.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T408S_b19_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 - SL297_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T45_b19_Skin_PCW17.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T45_b19_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 - SL297_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T11_b19_Skin_PCW19.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T11_b19_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 - SL298_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T187_b19_Skin_PCW23.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T187_b19_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 - SL298_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T299_b19_Scalp_PCW21.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T299_b19_Scalp_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 - SL298_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T408S_b19_Skin_PCW19.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T408S_b19_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 - SL298_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T45_b19_Skin_PCW17.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T45_b19_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 - SL298_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T108_b20_Kidney_PCW17.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T108_b20_Kidney_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 - SL305_kidney_atac_redo.T108_b20_Kidney_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T181_b20_Kidney_PCW19.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T181_b20_Kidney_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 - SL305_kidney_atac_redo.T181_b20_Kidney_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T271_b20_Kidney_PCW18.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T271_b20_Kidney_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 - SL305_kidney_atac_redo.T271_b20_Kidney_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T309_b20_Kidney_PCW21.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T309_b20_Kidney_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 - SL305_kidney_atac_redo.T309_b20_Kidney_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T359_b20_Kidney_PCW20.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T359_b20_Kidney_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 - SL305_kidney_atac_redo.T359_b20_Kidney_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T373_b20_Kidney_PCW15.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T373_b20_Kidney_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 - SL305_kidney_atac_redo.T373_b20_Kidney_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T42_b20_Kidney_PCW17.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T42_b20_Kidney_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 - SL305_kidney_atac_redo.T42_b20_Kidney_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T65_b20_Kidney_PCW18.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T65_b20_Kidney_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 - SL305_kidney_atac_redo.T65_b20_Kidney_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T108_b20_Kidney_PCW17.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T108_b20_Kidney_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 - SL306_kidney_atac_redo.T108_b20_Kidney_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T181_b20_Kidney_PCW19.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T181_b20_Kidney_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 - SL306_kidney_atac_redo.T181_b20_Kidney_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T271_b20_Kidney_PCW18.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T271_b20_Kidney_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 - SL306_kidney_atac_redo.T271_b20_Kidney_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T309_b20_Kidney_PCW21.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T309_b20_Kidney_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 - SL306_kidney_atac_redo.T309_b20_Kidney_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T359_b20_Kidney_PCW20.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T359_b20_Kidney_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 - SL306_kidney_atac_redo.T359_b20_Kidney_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T373_b20_Kidney_PCW15.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T373_b20_Kidney_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 - SL306_kidney_atac_redo.T373_b20_Kidney_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T42_b20_Kidney_PCW17.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T42_b20_Kidney_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 - SL306_kidney_atac_redo.T42_b20_Kidney_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T65_b20_Kidney_PCW18.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T65_b20_Kidney_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 - SL306_kidney_atac_redo.T65_b20_Kidney_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL281_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL281_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL281_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T175_b18_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T198_b18_Lung_PCW23.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T24_b18_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T305_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T333_b18_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T49_b18_Lung_PCW20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL282_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end1.fastq.gz SL282_b18_ATAC_lungredo2.barcodes_annotated.T77_b18_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL282_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T11_b19_Skin_PCW19.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T11_b19_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 - SL297_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T187_b19_Skin_PCW23.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T187_b19_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 - SL297_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T299_b19_Scalp_PCW21.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T299_b19_Scalp_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 - SL297_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T408S_b19_Skin_PCW19.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T408S_b19_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 - SL297_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL297_skin_atac_redo.barcodes_annotated.T45_b19_Skin_PCW17.end1.fastq.gz SL297_skin_atac_redo.barcodes_annotated.T45_b19_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 - SL297_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T11_b19_Skin_PCW19.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T11_b19_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 - SL298_skin_atac_redo.T11_b19_Skin_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T187_b19_Skin_PCW23.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T187_b19_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 - SL298_skin_atac_redo.T187_b19_Skin_PCW23.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T299_b19_Scalp_PCW21.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T299_b19_Scalp_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 - SL298_skin_atac_redo.T299_b19_Scalp_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T408S_b19_Skin_PCW19.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T408S_b19_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 - SL298_skin_atac_redo.T408S_b19_Skin_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL298_skin_atac_redo.barcodes_annotated.T45_b19_Skin_PCW17.end1.fastq.gz SL298_skin_atac_redo.barcodes_annotated.T45_b19_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 - SL298_skin_atac_redo.T45_b19_Skin_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T108_b20_Kidney_PCW17.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T108_b20_Kidney_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 - SL305_kidney_atac_redo.T108_b20_Kidney_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T181_b20_Kidney_PCW19.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T181_b20_Kidney_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 - SL305_kidney_atac_redo.T181_b20_Kidney_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T271_b20_Kidney_PCW18.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T271_b20_Kidney_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 - SL305_kidney_atac_redo.T271_b20_Kidney_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T309_b20_Kidney_PCW21.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T309_b20_Kidney_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 - SL305_kidney_atac_redo.T309_b20_Kidney_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T359_b20_Kidney_PCW20.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T359_b20_Kidney_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 - SL305_kidney_atac_redo.T359_b20_Kidney_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T373_b20_Kidney_PCW15.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T373_b20_Kidney_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 - SL305_kidney_atac_redo.T373_b20_Kidney_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T42_b20_Kidney_PCW17.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T42_b20_Kidney_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 - SL305_kidney_atac_redo.T42_b20_Kidney_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL305_kidney_atac_redo.barcodes_annotated.T65_b20_Kidney_PCW18.end1.fastq.gz SL305_kidney_atac_redo.barcodes_annotated.T65_b20_Kidney_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 - SL305_kidney_atac_redo.T65_b20_Kidney_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T108_b20_Kidney_PCW17.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T108_b20_Kidney_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 - SL306_kidney_atac_redo.T108_b20_Kidney_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T181_b20_Kidney_PCW19.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T181_b20_Kidney_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 - SL306_kidney_atac_redo.T181_b20_Kidney_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T271_b20_Kidney_PCW18.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T271_b20_Kidney_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 - SL306_kidney_atac_redo.T271_b20_Kidney_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T309_b20_Kidney_PCW21.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T309_b20_Kidney_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 - SL306_kidney_atac_redo.T309_b20_Kidney_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T359_b20_Kidney_PCW20.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T359_b20_Kidney_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 - SL306_kidney_atac_redo.T359_b20_Kidney_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T373_b20_Kidney_PCW15.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T373_b20_Kidney_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 - SL306_kidney_atac_redo.T373_b20_Kidney_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T42_b20_Kidney_PCW17.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T42_b20_Kidney_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 - SL306_kidney_atac_redo.T42_b20_Kidney_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL306_kidney_atac_redo.barcodes_annotated.T65_b20_Kidney_PCW18.end1.fastq.gz SL306_kidney_atac_redo.barcodes_annotated.T65_b20_Kidney_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 - SL306_kidney_atac_redo.T65_b20_Kidney_PCW18.2x36mers.hg38.unique