python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL145_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL146_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL147_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL148_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL149_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL150_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL151_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL152_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL145_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL146_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL147_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL148_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL149_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL150_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL151_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL152_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL145_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL146_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL147_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL148_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL149_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL150_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL151_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T014_b11_Heart_PCW.end2.fastq.gz -trim 36 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 - SL152_b11_ATAC_HeartRedo.T014_b11_Heart_PCW.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL145_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL146_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL147_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL148_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL149_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL150_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL151_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T032_b11_Heart_PCW12.end2.fastq.gz -trim 36 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 - SL152_b11_ATAC_HeartRedo.T032_b11_Heart_PCW12.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_PCW17.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T104_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T104_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_PCW17.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T30_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T30_b11_Heart_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_PCW20.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T361_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T361_b11_Heart_PCW20.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_PCW15.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T379_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T379_b11_Heart_PCW15.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_PCW19.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T407_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T407_b11_Heart_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL145_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL145_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL146_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL146_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL147_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL147_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL148_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL148_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL149_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL149_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL150_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL150_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL151_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL151_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_PCW18.end1.fastq.gz SL152_b11_ATAC_HeartRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T92_b11_Heart_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 - SL152_b11_ATAC_HeartRedo.T92_b11_Heart_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T286_b12_Lung_PCW14.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T132_b12_lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T107_b12_Lung_PCW17.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T256_b12_Lung_PCW18.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T408L_b12_Lung_PCW19.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T226_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T304_b12_Lung_PCW21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL153_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL153_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL154_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL154_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL155_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL155_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL156_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL156_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL157_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL157_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL158_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL158_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL159_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end1.fastq.gz SL160_b12_ATAC_LungRedo.230206_A00509_0673_AHNJMCDSX5.barcodes_annotated.T164_b12_Lung_PCW10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SL160_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique