python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_5-6ss_rep1_ATAC-seq-GSM3431430.end1.fastq.gz non-neural_crest_5-6ss_rep1_ATAC-seq-GSM3431430.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 - non-neural_crest_5-6ss_rep1_ATAC-seq-GSM3431430.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_5-6ss_rep2_ATAC-seq-GSM3431431.end1.fastq.gz non-neural_crest_5-6ss_rep2_ATAC-seq-GSM3431431.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 - non-neural_crest_5-6ss_rep2_ATAC-seq-GSM3431431.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_5-6ss_rep1_ATAC-seq-GSM3431430.end1.fastq.gz non-neural_crest_5-6ss_rep1_ATAC-seq-GSM3431430.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 - non-neural_crest_5-6ss_rep1_ATAC-seq-GSM3431430.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_5-6ss_rep2_ATAC-seq-GSM3431431.end1.fastq.gz non-neural_crest_5-6ss_rep2_ATAC-seq-GSM3431431.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 - non-neural_crest_5-6ss_rep2_ATAC-seq-GSM3431431.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_5-6ss_rep4_ATAC-seq-GSM3431433.end1.fastq.gz non-neural_crest_5-6ss_rep4_ATAC-seq-GSM3431433.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 - non-neural_crest_5-6ss_rep4_ATAC-seq-GSM3431433.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_8-10ss_rep1_ATAC-seq-GSM3431434.end1.fastq.gz non-neural_crest_8-10ss_rep1_ATAC-seq-GSM3431434.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 - non-neural_crest_8-10ss_rep1_ATAC-seq-GSM3431434.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_8-10ss_rep2_ATAC-seq-GSM3431435.end1.fastq.gz non-neural_crest_8-10ss_rep2_ATAC-seq-GSM3431435.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 - non-neural_crest_8-10ss_rep2_ATAC-seq-GSM3431435.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-5-6ss_FoxD3_rep1_ATAC-seq-GSM3431421.end1.fastq.gz neural_crest-5-6ss_FoxD3_rep1_ATAC-seq-GSM3431421.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 - neural_crest-5-6ss_FoxD3_rep1_ATAC-seq-GSM3431421.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_5-6ss_rep4_ATAC-seq-GSM3431433.end1.fastq.gz non-neural_crest_5-6ss_rep4_ATAC-seq-GSM3431433.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 - non-neural_crest_5-6ss_rep4_ATAC-seq-GSM3431433.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_8-10ss_rep1_ATAC-seq-GSM3431434.end1.fastq.gz non-neural_crest_8-10ss_rep1_ATAC-seq-GSM3431434.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 - non-neural_crest_8-10ss_rep1_ATAC-seq-GSM3431434.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_8-10ss_rep2_ATAC-seq-GSM3431435.end1.fastq.gz non-neural_crest_8-10ss_rep2_ATAC-seq-GSM3431435.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 - non-neural_crest_8-10ss_rep2_ATAC-seq-GSM3431435.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-5-6ss_FoxD3_rep1_ATAC-seq-GSM3431421.end1.fastq.gz neural_crest-5-6ss_FoxD3_rep1_ATAC-seq-GSM3431421.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 - neural_crest-5-6ss_FoxD3_rep1_ATAC-seq-GSM3431421.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-5-6ss_FoxD3_rep2_ATAC-seq-GSM3431422.end1.fastq.gz neural_crest-5-6ss_FoxD3_rep2_ATAC-seq-GSM3431422.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 - neural_crest-5-6ss_FoxD3_rep2_ATAC-seq-GSM3431422.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-5-6ss_Pax7_ATAC-seq-GSM3431423.end1.fastq.gz neural_crest-5-6ss_Pax7_ATAC-seq-GSM3431423.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 - neural_crest-5-6ss_Pax7_ATAC-seq-GSM3431423.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py whole_epiblast_rep1_ATAC-seq-GSM3431425.end1.fastq.gz whole_epiblast_rep1_ATAC-seq-GSM3431425.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 - whole_epiblast_rep1_ATAC-seq-GSM3431425.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-8-10ss_FoxD3_rep3_ATAC-seq-GSM3431429.end1.fastq.gz neural_crest-8-10ss_FoxD3_rep3_ATAC-seq-GSM3431429.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 - neural_crest-8-10ss_FoxD3_rep3_ATAC-seq-GSM3431429.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-5-6ss_FoxD3_rep2_ATAC-seq-GSM3431422.end1.fastq.gz neural_crest-5-6ss_FoxD3_rep2_ATAC-seq-GSM3431422.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 - neural_crest-5-6ss_FoxD3_rep2_ATAC-seq-GSM3431422.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-5-6ss_Pax7_ATAC-seq-GSM3431423.end1.fastq.gz neural_crest-5-6ss_Pax7_ATAC-seq-GSM3431423.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 - neural_crest-5-6ss_Pax7_ATAC-seq-GSM3431423.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py whole_epiblast_rep1_ATAC-seq-GSM3431425.end1.fastq.gz whole_epiblast_rep1_ATAC-seq-GSM3431425.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 - whole_epiblast_rep1_ATAC-seq-GSM3431425.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-8-10ss_FoxD3_rep3_ATAC-seq-GSM3431429.end1.fastq.gz neural_crest-8-10ss_FoxD3_rep3_ATAC-seq-GSM3431429.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 - neural_crest-8-10ss_FoxD3_rep3_ATAC-seq-GSM3431429.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_5-6ss_rep3_ATAC-seq-GSM3431432.end1.fastq.gz non-neural_crest_5-6ss_rep3_ATAC-seq-GSM3431432.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 - non-neural_crest_5-6ss_rep3_ATAC-seq-GSM3431432.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_8-10ss_rep3_ATAC-seq-GSM3431436.end1.fastq.gz non-neural_crest_8-10ss_rep3_ATAC-seq-GSM3431436.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 - non-neural_crest_8-10ss_rep3_ATAC-seq-GSM3431436.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_8-10ss_rep4_ATAC-seq-GSM3431437.end1.fastq.gz non-neural_crest_8-10ss_rep4_ATAC-seq-GSM3431437.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 - non-neural_crest_8-10ss_rep4_ATAC-seq-GSM3431437.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HH10_somites_ATAC-seq-GSM3431424.end1.fastq.gz HH10_somites_ATAC-seq-GSM3431424.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 - HH10_somites_ATAC-seq-GSM3431424.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_5-6ss_rep3_ATAC-seq-GSM3431432.end1.fastq.gz non-neural_crest_5-6ss_rep3_ATAC-seq-GSM3431432.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 - non-neural_crest_5-6ss_rep3_ATAC-seq-GSM3431432.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_8-10ss_rep3_ATAC-seq-GSM3431436.end1.fastq.gz non-neural_crest_8-10ss_rep3_ATAC-seq-GSM3431436.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 - non-neural_crest_8-10ss_rep3_ATAC-seq-GSM3431436.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py non-neural_crest_8-10ss_rep4_ATAC-seq-GSM3431437.end1.fastq.gz non-neural_crest_8-10ss_rep4_ATAC-seq-GSM3431437.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 - non-neural_crest_8-10ss_rep4_ATAC-seq-GSM3431437.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HH10_somites_ATAC-seq-GSM3431424.end1.fastq.gz HH10_somites_ATAC-seq-GSM3431424.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 - HH10_somites_ATAC-seq-GSM3431424.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py whole_epiblast_rep2_ATAC-seq-GSM3431426.end1.fastq.gz whole_epiblast_rep2_ATAC-seq-GSM3431426.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 - whole_epiblast_rep2_ATAC-seq-GSM3431426.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-8-10ss_FoxD3_rep1_ATAC-seq-GSM3431427.end1.fastq.gz neural_crest-8-10ss_FoxD3_rep1_ATAC-seq-GSM3431427.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 - neural_crest-8-10ss_FoxD3_rep1_ATAC-seq-GSM3431427.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-8-10ss_FoxD3_rep2_ATAC-seq-GSM3431428.end1.fastq.gz neural_crest-8-10ss_FoxD3_rep2_ATAC-seq-GSM3431428.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 - neural_crest-8-10ss_FoxD3_rep2_ATAC-seq-GSM3431428.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py whole_epiblast_rep2_ATAC-seq-GSM3431426.end1.fastq.gz whole_epiblast_rep2_ATAC-seq-GSM3431426.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 - whole_epiblast_rep2_ATAC-seq-GSM3431426.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-8-10ss_FoxD3_rep1_ATAC-seq-GSM3431427.end1.fastq.gz neural_crest-8-10ss_FoxD3_rep1_ATAC-seq-GSM3431427.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 - neural_crest-8-10ss_FoxD3_rep1_ATAC-seq-GSM3431427.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py neural_crest-8-10ss_FoxD3_rep2_ATAC-seq-GSM3431428.end1.fastq.gz neural_crest-8-10ss_FoxD3_rep2_ATAC-seq-GSM3431428.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 - neural_crest-8-10ss_FoxD3_rep2_ATAC-seq-GSM3431428.2x36mers.Gallus_gallus.GRCg6a.dna.toplevel.unique