python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C4955_atac_seq-GSM3464044.end1.fastq.gz C4955_atac_seq-GSM3464044.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C4955_atac_seq-GSM3464044.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C8861_atac_seq-GSM3464045.end1.fastq.gz C8861_atac_seq-GSM3464045.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C8861_atac_seq-GSM3464045.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C4955_atac_seq-GSM3464044.end1.fastq.gz C4955_atac_seq-GSM3464044.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C4955_atac_seq-GSM3464044.2x36mers.Pan_troglodytes.CHIMP2.1.4.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C8861_atac_seq-GSM3464045.end1.fastq.gz C8861_atac_seq-GSM3464045.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C8861_atac_seq-GSM3464045.2x36mers.Pan_troglodytes.CHIMP2.1.4.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3647_atac_seq-GSM3464041-all.end1.fastq.gz C3647_atac_seq-GSM3464041-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3647_atac_seq-GSM3464041-all.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3649_atac_seq-GSM3464042.end1.fastq.gz C3649_atac_seq-GSM3464042.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3649_atac_seq-GSM3464042.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3647_atac_seq-GSM3464041-all.end1.fastq.gz C3647_atac_seq-GSM3464041-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3647_atac_seq-GSM3464041-all.2x36mers.Pan_troglodytes.CHIMP2.1.4.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3649_atac_seq-GSM3464042.end1.fastq.gz C3649_atac_seq-GSM3464042.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3649_atac_seq-GSM3464042.2x36mers.Pan_troglodytes.CHIMP2.1.4.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3651_atac_seq-GSM3464043-all.end1.fastq.gz C3651_atac_seq-GSM3464043-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3651_atac_seq-GSM3464043-all.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C40280_atac_seq-GSM3464046-all.end1.fastq.gz C40280_atac_seq-GSM3464046-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C40280_atac_seq-GSM3464046-all.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3651_atac_seq-GSM3464043-all.end1.fastq.gz C3651_atac_seq-GSM3464043-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3651_atac_seq-GSM3464043-all.2x36mers.Pan_troglodytes.CHIMP2.1.4.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C40280_atac_seq-GSM3464046-all.end1.fastq.gz C40280_atac_seq-GSM3464046-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Pan_troglodytes.CHIMP2.1.4/bowtie-indexes/Pan_troglodytes.CHIMP2.1.4.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C40280_atac_seq-GSM3464046-all.2x36mers.Pan_troglodytes.CHIMP2.1.4.dna.toplevel.unique