python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH20_replicate_2-GSM5017898.end1.fastq.gz ATAC-seq_wing_bud_HH20_replicate_2-GSM5017898.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 - ATAC-seq_wing_bud_HH20_replicate_2-GSM5017898.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH22_replicate_1-GSM5017899.end1.fastq.gz ATAC-seq_wing_bud_HH22_replicate_1-GSM5017899.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 - ATAC-seq_wing_bud_HH22_replicate_1-GSM5017899.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH20_replicate_2-GSM5017898.end1.fastq.gz ATAC-seq_wing_bud_HH20_replicate_2-GSM5017898.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 - ATAC-seq_wing_bud_HH20_replicate_2-GSM5017898.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH22_replicate_1-GSM5017899.end1.fastq.gz ATAC-seq_wing_bud_HH22_replicate_1-GSM5017899.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 - ATAC-seq_wing_bud_HH22_replicate_1-GSM5017899.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH24_replicate_1-GSM5017901.end1.fastq.gz ATAC-seq_wing_bud_HH24_replicate_1-GSM5017901.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 - ATAC-seq_wing_bud_HH24_replicate_1-GSM5017901.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH20_replicate_1-GSM5017897.end1.fastq.gz ATAC-seq_wing_bud_HH20_replicate_1-GSM5017897.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 - ATAC-seq_wing_bud_HH20_replicate_1-GSM5017897.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH22_replicate_2-GSM5017900.end1.fastq.gz ATAC-seq_wing_bud_HH22_replicate_2-GSM5017900.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 - ATAC-seq_wing_bud_HH22_replicate_2-GSM5017900.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH24_replicate_2-GSM5017902.end1.fastq.gz ATAC-seq_wing_bud_HH24_replicate_2-GSM5017902.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 - ATAC-seq_wing_bud_HH24_replicate_2-GSM5017902.2x36mers.MT        
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH24_replicate_1-GSM5017901.end1.fastq.gz ATAC-seq_wing_bud_HH24_replicate_1-GSM5017901.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 - ATAC-seq_wing_bud_HH24_replicate_1-GSM5017901.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH20_replicate_1-GSM5017897.end1.fastq.gz ATAC-seq_wing_bud_HH20_replicate_1-GSM5017897.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 - ATAC-seq_wing_bud_HH20_replicate_1-GSM5017897.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH22_replicate_2-GSM5017900.end1.fastq.gz ATAC-seq_wing_bud_HH22_replicate_2-GSM5017900.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 - ATAC-seq_wing_bud_HH22_replicate_2-GSM5017900.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_wing_bud_HH24_replicate_2-GSM5017902.end1.fastq.gz ATAC-seq_wing_bud_HH24_replicate_2-GSM5017902.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 - ATAC-seq_wing_bud_HH24_replicate_2-GSM5017902.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique