python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_1_Fat_ATAC-GSM4256374.end1.fastq.gz Duroc_2W_1_Fat_ATAC-GSM4256374.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_1_Fat_ATAC-GSM4256374.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_2_Fat_ATAC-GSM4256375.end1.fastq.gz Duroc_2W_2_Fat_ATAC-GSM4256375.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_2_Fat_ATAC-GSM4256375.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_1_Heart_ATAC-GSM4256376.end1.fastq.gz Duroc_2W_1_Heart_ATAC-GSM4256376.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_1_Heart_ATAC-GSM4256376.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_2_Heart_ATAC-GSM4256377.end1.fastq.gz Duroc_2W_2_Heart_ATAC-GSM4256377.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_2_Heart_ATAC-GSM4256377.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_1_Liver_ATAC-GSM4256378.end1.fastq.gz Duroc_2W_1_Liver_ATAC-GSM4256378.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_1_Liver_ATAC-GSM4256378.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_2_Liver_ATAC-GSM4256379.end1.fastq.gz Duroc_2W_2_Liver_ATAC-GSM4256379.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_2_Liver_ATAC-GSM4256379.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_1_Muscle_ATAC-GSM4256380.end1.fastq.gz Duroc_2W_1_Muscle_ATAC-GSM4256380.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_1_Muscle_ATAC-GSM4256380.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_2_Muscle_ATAC-GSM4256381.end1.fastq.gz Duroc_2W_2_Muscle_ATAC-GSM4256381.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_2_Muscle_ATAC-GSM4256381.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Duroc_2W_1_Spleen_ATAC-GSM4256382.end1.fastq.gz Duroc_2W_1_Spleen_ATAC-GSM4256382.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Duroc_2W_1_Spleen_ATAC-GSM4256382.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ES_2W_1_Fat_ATAC-GSM4256383.end1.fastq.gz ES_2W_1_Fat_ATAC-GSM4256383.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ES_2W_1_Fat_ATAC-GSM4256383.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ES_2W_2_Fat_ATAC-GSM4256384.end1.fastq.gz ES_2W_2_Fat_ATAC-GSM4256384.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ES_2W_2_Fat_ATAC-GSM4256384.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ES_2W_1_Heart_ATAC-GSM4256385.end1.fastq.gz ES_2W_1_Heart_ATAC-GSM4256385.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ES_2W_1_Heart_ATAC-GSM4256385.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ES_2W_2_Liver_ATAC-GSM4256387.end1.fastq.gz ES_2W_2_Liver_ATAC-GSM4256387.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ES_2W_2_Liver_ATAC-GSM4256387.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ES_2W_1_Muscle_ATAC-GSM4256388.end1.fastq.gz ES_2W_1_Muscle_ATAC-GSM4256388.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ES_2W_1_Muscle_ATAC-GSM4256388.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ES_2W_2_Muscle_ATAC-GSM4256389.end1.fastq.gz ES_2W_2_Muscle_ATAC-GSM4256389.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ES_2W_2_Muscle_ATAC-GSM4256389.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ES_2W_1_Spleen_ATAC-GSM4256390.end1.fastq.gz ES_2W_1_Spleen_ATAC-GSM4256390.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ES_2W_1_Spleen_ATAC-GSM4256390.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LW_2W_1_Fat_ATAC-GSM4256391.end1.fastq.gz LW_2W_1_Fat_ATAC-GSM4256391.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LW_2W_1_Fat_ATAC-GSM4256391.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LW_2W_2_Fat_ATAC-GSM4256392.end1.fastq.gz LW_2W_2_Fat_ATAC-GSM4256392.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LW_2W_2_Fat_ATAC-GSM4256392.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LW_2W_1_Liver_ATAC-GSM4256393.end1.fastq.gz LW_2W_1_Liver_ATAC-GSM4256393.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LW_2W_1_Liver_ATAC-GSM4256393.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LW_2W_1_Muscle_ATAC-GSM4256395.end1.fastq.gz LW_2W_1_Muscle_ATAC-GSM4256395.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LW_2W_1_Muscle_ATAC-GSM4256395.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LW_2W_2_Muscle_ATAC-GSM4256396.end1.fastq.gz LW_2W_2_Muscle_ATAC-GSM4256396.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LW_2W_2_Muscle_ATAC-GSM4256396.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MS_2W_1_Fat_ATAC-GSM4256397.end1.fastq.gz MS_2W_1_Fat_ATAC-GSM4256397.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MS_2W_1_Fat_ATAC-GSM4256397.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MS_2W_2_Fat_ATAC-GSM4256398.end1.fastq.gz MS_2W_2_Fat_ATAC-GSM4256398.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MS_2W_2_Fat_ATAC-GSM4256398.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MS_2W_2_Liver_ATAC-GSM4256400.end1.fastq.gz MS_2W_2_Liver_ATAC-GSM4256400.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MS_2W_2_Liver_ATAC-GSM4256400.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MS_2W_2_Muscle_ATAC-GSM4256401.end1.fastq.gz MS_2W_2_Muscle_ATAC-GSM4256401.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/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel -p 20 -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 -F 4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sus_scrofa-Sscrofa11.1/bowtie-indexes/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MS_2W_2_Muscle_ATAC-GSM4256401.2x36mers.noMT.unique