python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GSM8216264-fetal-Rumen-1.end1.fastq.gz GSM8216264-fetal-Rumen-1.end2.fastq.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/MT -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GSM8216264-fetal-Rumen-1.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GSM8216265-fetal-Rumen-2.end1.fastq.gz GSM8216265-fetal-Rumen-2.end2.fastq.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/MT -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GSM8216265-fetal-Rumen-2.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GSM8216266-adult-Rumen-1.end1.fastq.gz GSM8216266-adult-Rumen-1.end2.fastq.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/MT -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GSM8216266-adult-Rumen-1.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GSM8216267-adult-Rumen-2.end1.fastq.gz GSM8216267-adult-Rumen-2.end2.fastq.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/MT -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GSM8216267-adult-Rumen-2.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GSM8216264-fetal-Rumen-1.end1.fastq.gz GSM8216264-fetal-Rumen-1.end2.fastq.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GSM8216264-fetal-Rumen-1.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GSM8216265-fetal-Rumen-2.end1.fastq.gz GSM8216265-fetal-Rumen-2.end2.fastq.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GSM8216265-fetal-Rumen-2.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GSM8216266-adult-Rumen-1.end1.fastq.gz GSM8216266-adult-Rumen-1.end2.fastq.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GSM8216266-adult-Rumen-1.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GSM8216267-adult-Rumen-2.end1.fastq.gz GSM8216267-adult-Rumen-2.end2.fastq.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GSM8216267-adult-Rumen-2.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique