python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECLP2-GSM7053857.end1.fastq.gz MECLP2-GSM7053857.end2.fastq.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/Capra_hircus-ARS1.2/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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECLP2-GSM7053857.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECLP5-GSM7053858.end1.fastq.gz MECLP5-GSM7053858.end2.fastq.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/Capra_hircus-ARS1.2/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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECLP5-GSM7053858.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECLP2-GSM7053857.end1.fastq.gz MECLP2-GSM7053857.end2.fastq.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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005044.2 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECLP2-GSM7053857.2x36mers.Capra_hircus-ARS1.2.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECLP5-GSM7053858.end1.fastq.gz MECLP5-GSM7053858.end2.fastq.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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005044.2 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECLP5-GSM7053858.2x36mers.Capra_hircus-ARS1.2.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECDP3-GSM7053855.end1.fastq.gz MECDP3-GSM7053855.end2.fastq.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/Capra_hircus-ARS1.2/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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECDP3-GSM7053855.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECDP2-GSM7053854.end1.fastq.gz MECDP2-GSM7053854.end2.fastq.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/Capra_hircus-ARS1.2/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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECDP2-GSM7053854.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECDP1-GSM7053853.end1.fastq.gz MECDP1-GSM7053853.end2.fastq.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/Capra_hircus-ARS1.2/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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECDP1-GSM7053853.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECDP3-GSM7053855.end1.fastq.gz MECDP3-GSM7053855.end2.fastq.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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005044.2 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECDP3-GSM7053855.2x36mers.Capra_hircus-ARS1.2.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECDP2-GSM7053854.end1.fastq.gz MECDP2-GSM7053854.end2.fastq.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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005044.2 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECDP2-GSM7053854.2x36mers.Capra_hircus-ARS1.2.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MECDP1-GSM7053853.end1.fastq.gz MECDP1-GSM7053853.end2.fastq.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/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005044.2 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Capra_hircus-ARS1.2/bowtie-indexes/Capra_hircus-ARS1.2.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MECDP1-GSM7053853.2x36mers.Capra_hircus-ARS1.2.unique