python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py term_rep1-GSM4987806.end1.fastq.gz term_rep1-GSM4987806.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - term_rep1-GSM4987806.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py term_rep3-GSM4987808.end1.fastq.gz term_rep3-GSM4987808.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - term_rep3-GSM4987808.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py term_rep1-GSM4987806.end1.fastq.gz term_rep1-GSM4987806.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - term_rep1-GSM4987806.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py term_rep3-GSM4987808.end1.fastq.gz term_rep3-GSM4987808.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - term_rep3-GSM4987808.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py IMV_rep1-GSM4987809.end1.fastq.gz IMV_rep1-GSM4987809.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - IMV_rep1-GSM4987809.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py IMV_rep4-GSM4987812.end1.fastq.gz IMV_rep4-GSM4987812.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - IMV_rep4-GSM4987812.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep4-GSM4987816.end1.fastq.gz NRS_rep4-GSM4987816.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep4-GSM4987816.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py fetal_end_rep2-GSM4987821.end1.fastq.gz fetal_end_rep2-GSM4987821.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - fetal_end_rep2-GSM4987821.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py IMV_rep1-GSM4987809.end1.fastq.gz IMV_rep1-GSM4987809.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - IMV_rep1-GSM4987809.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py IMV_rep4-GSM4987812.end1.fastq.gz IMV_rep4-GSM4987812.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - IMV_rep4-GSM4987812.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep4-GSM4987816.end1.fastq.gz NRS_rep4-GSM4987816.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep4-GSM4987816.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py fetal_end_rep2-GSM4987821.end1.fastq.gz fetal_end_rep2-GSM4987821.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - fetal_end_rep2-GSM4987821.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py term_rep2-GSM4987807.end1.fastq.gz term_rep2-GSM4987807.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - term_rep2-GSM4987807.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py IMV_rep2-GSM4987810.end1.fastq.gz IMV_rep2-GSM4987810.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - IMV_rep2-GSM4987810.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py term_rep2-GSM4987807.end1.fastq.gz term_rep2-GSM4987807.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - term_rep2-GSM4987807.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py IMV_rep2-GSM4987810.end1.fastq.gz IMV_rep2-GSM4987810.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - IMV_rep2-GSM4987810.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py IMV_rep3-GSM4987811.end1.fastq.gz IMV_rep3-GSM4987811.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - IMV_rep3-GSM4987811.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep2-GSM4987814.end1.fastq.gz NRS_rep2-GSM4987814.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep2-GSM4987814.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep3-GSM4987815.end1.fastq.gz NRS_rep3-GSM4987815.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep3-GSM4987815.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep5-GSM4987817.end1.fastq.gz NRS_rep5-GSM4987817.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep5-GSM4987817.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py IMV_rep3-GSM4987811.end1.fastq.gz IMV_rep3-GSM4987811.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - IMV_rep3-GSM4987811.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep2-GSM4987814.end1.fastq.gz NRS_rep2-GSM4987814.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep2-GSM4987814.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep3-GSM4987815.end1.fastq.gz NRS_rep3-GSM4987815.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep3-GSM4987815.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep5-GSM4987817.end1.fastq.gz NRS_rep5-GSM4987817.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep5-GSM4987817.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py fetal_start_rep2-GSM4987819.end1.fastq.gz fetal_start_rep2-GSM4987819.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - fetal_start_rep2-GSM4987819.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep1-GSM4987813.end1.fastq.gz NRS_rep1-GSM4987813.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep1-GSM4987813.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py fetal_end_rep1-GSM4987820.end1.fastq.gz fetal_end_rep1-GSM4987820.end2.fastq.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/Ovis_aries.Oar_v3.1/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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - fetal_end_rep1-GSM4987820.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py fetal_start_rep2-GSM4987819.end1.fastq.gz fetal_start_rep2-GSM4987819.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - fetal_start_rep2-GSM4987819.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NRS_rep1-GSM4987813.end1.fastq.gz NRS_rep1-GSM4987813.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NRS_rep1-GSM4987813.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py fetal_end_rep1-GSM4987820.end1.fastq.gz fetal_end_rep1-GSM4987820.end2.fastq.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.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/Ovis_aries.Oar_v3.1/bowtie-indexes/Ovis_aries.Oar_v3.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - fetal_end_rep1-GSM4987820.2x36mers.Ovis_aries.Oar_v3.1.dna.toplevel.unique