python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_flank_rep2-GSM4057719.end1.fastq.gz Chick_HH18_flank_rep2-GSM4057719.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_flank_rep2-GSM4057719.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_forelimb_rep1-GSM4057721.end1.fastq.gz Chick_HH18_forelimb_rep1-GSM4057721.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_forelimb_rep1-GSM4057721.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_flank_rep2-GSM4057719.end1.fastq.gz Chick_HH18_flank_rep2-GSM4057719.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_flank_rep2-GSM4057719.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_forelimb_rep1-GSM4057721.end1.fastq.gz Chick_HH18_forelimb_rep1-GSM4057721.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_forelimb_rep1-GSM4057721.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_forelimb_rep2-GSM4057722.end1.fastq.gz Chick_HH18_forelimb_rep2-GSM4057722.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_forelimb_rep2-GSM4057722.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_forelimb_rep3-GSM4057723.end1.fastq.gz Chick_HH18_forelimb_rep3-GSM4057723.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_forelimb_rep3-GSM4057723.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_hindlimb_rep1-GSM4057724.end1.fastq.gz Chick_HH18_hindlimb_rep1-GSM4057724.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_hindlimb_rep1-GSM4057724.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_hindlimb_rep3-GSM4057726.end1.fastq.gz Chick_HH18_hindlimb_rep3-GSM4057726.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_hindlimb_rep3-GSM4057726.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_forelimb_rep2-GSM4057722.end1.fastq.gz Chick_HH18_forelimb_rep2-GSM4057722.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_forelimb_rep2-GSM4057722.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_forelimb_rep3-GSM4057723.end1.fastq.gz Chick_HH18_forelimb_rep3-GSM4057723.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_forelimb_rep3-GSM4057723.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_hindlimb_rep1-GSM4057724.end1.fastq.gz Chick_HH18_hindlimb_rep1-GSM4057724.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_hindlimb_rep1-GSM4057724.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_hindlimb_rep3-GSM4057726.end1.fastq.gz Chick_HH18_hindlimb_rep3-GSM4057726.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_hindlimb_rep3-GSM4057726.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_flank_rep1-GSM4057718.end1.fastq.gz Chick_HH18_flank_rep1-GSM4057718.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_flank_rep1-GSM4057718.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_hindlimb_rep2-GSM4057725.end1.fastq.gz Chick_HH18_hindlimb_rep2-GSM4057725.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_hindlimb_rep2-GSM4057725.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_flank_rep3-GSM4057720.end1.fastq.gz Chick_HH18_flank_rep3-GSM4057720.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/Gallus_gallus-GRCg6a/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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_flank_rep3-GSM4057720.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_flank_rep1-GSM4057718.end1.fastq.gz Chick_HH18_flank_rep1-GSM4057718.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_flank_rep1-GSM4057718.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_hindlimb_rep2-GSM4057725.end1.fastq.gz Chick_HH18_hindlimb_rep2-GSM4057725.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_hindlimb_rep2-GSM4057725.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Chick_HH18_flank_rep3-GSM4057720.end1.fastq.gz Chick_HH18_flank_rep3-GSM4057720.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/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.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/Birds/Gallus_gallus-GRCg6a/bowtie-indexes/Gallus_gallus.GRCg6a.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Chick_HH18_flank_rep3-GSM4057720.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique