python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_flank_rep1-GSM4057727.end1.fastq.gz Emu_HH18_flank_rep1-GSM4057727.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_flank_rep1-GSM4057727.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_flank_rep2-GSM4057728.end1.fastq.gz Emu_HH18_flank_rep2-GSM4057728.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_flank_rep2-GSM4057728.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_flank_rep3-GSM4057729.end1.fastq.gz Emu_HH18_flank_rep3-GSM4057729.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_flank_rep3-GSM4057729.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_forelimb_rep1-GSM4057730.end1.fastq.gz Emu_HH18_forelimb_rep1-GSM4057730.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_forelimb_rep1-GSM4057730.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_forelimb_rep2-GSM4057731.end1.fastq.gz Emu_HH18_forelimb_rep2-GSM4057731.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_forelimb_rep2-GSM4057731.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_forelimb_rep3-GSM4057732.end1.fastq.gz Emu_HH18_forelimb_rep3-GSM4057732.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_forelimb_rep3-GSM4057732.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_hindlimb_rep1-GSM4057733.end1.fastq.gz Emu_HH18_hindlimb_rep1-GSM4057733.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_hindlimb_rep1-GSM4057733.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_hindlimb_rep2-GSM4057734.end1.fastq.gz Emu_HH18_hindlimb_rep2-GSM4057734.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_hindlimb_rep2-GSM4057734.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Emu_HH18_hindlimb_rep3-GSM4057735.end1.fastq.gz Emu_HH18_hindlimb_rep3-GSM4057735.end2.fastq.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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1 -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/Birds/Dromaius_novaehollandiae-bDroNov1.hap1/bowtie-indexes/Dromaius_novaehollandiae-bDroNov1.hap1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Emu_HH18_hindlimb_rep3-GSM4057735.2x36mers.Dromaius_novaehollandiae-bDroNov1.hap1.unique