python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Heart-0day-rep1-ATAC-GSM7164788.end1.fastq.gz Heart-0day-rep1-ATAC-GSM7164788.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 - Heart-0day-rep1-ATAC-GSM7164788.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Heart-0day-rep2-ATAC-GSM7164789.end1.fastq.gz Heart-0day-rep2-ATAC-GSM7164789.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 - Heart-0day-rep2-ATAC-GSM7164789.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Kidney-0day-rep1-ATAC-GSM7164790.end1.fastq.gz Kidney-0day-rep1-ATAC-GSM7164790.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 - Kidney-0day-rep1-ATAC-GSM7164790.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Kidney-0day-rep2-ATAC-GSM7164791.end1.fastq.gz Kidney-0day-rep2-ATAC-GSM7164791.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 - Kidney-0day-rep2-ATAC-GSM7164791.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Lung-0day-rep1-ATAC-GSM7164792.end1.fastq.gz Lung-0day-rep1-ATAC-GSM7164792.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 - Lung-0day-rep1-ATAC-GSM7164792.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Lung-0day-rep2-ATAC-GSM7164793.end1.fastq.gz Lung-0day-rep2-ATAC-GSM7164793.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 - Lung-0day-rep2-ATAC-GSM7164793.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Muscle-0day-rep1-ATAC-GSM7164794.end1.fastq.gz Muscle-0day-rep1-ATAC-GSM7164794.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 - Muscle-0day-rep1-ATAC-GSM7164794.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Muscle-0day-rep2-ATAC-GSM7164795.end1.fastq.gz Muscle-0day-rep2-ATAC-GSM7164795.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 - Muscle-0day-rep2-ATAC-GSM7164795.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Spleen-0day-rep1-ATAC-GSM7164796.end1.fastq.gz Spleen-0day-rep1-ATAC-GSM7164796.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 - Spleen-0day-rep1-ATAC-GSM7164796.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Spleen-0day-rep2-ATAC-GSM7164797.end1.fastq.gz Spleen-0day-rep2-ATAC-GSM7164797.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 - Spleen-0day-rep2-ATAC-GSM7164797.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Liver-0day-rep1-ATAC-GSM7164798.end1.fastq.gz Liver-0day-rep1-ATAC-GSM7164798.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 - Liver-0day-rep1-ATAC-GSM7164798.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Liver-0day-rep2-ATAC-GSM7164799.end1.fastq.gz Liver-0day-rep2-ATAC-GSM7164799.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 - Liver-0day-rep2-ATAC-GSM7164799.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Liver-28day-rep1-ATAC-GSM7164800.end1.fastq.gz Liver-28day-rep1-ATAC-GSM7164800.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 - Liver-28day-rep1-ATAC-GSM7164800.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Liver-28day-rep2-ATAC-GSM7164801.end1.fastq.gz Liver-28day-rep2-ATAC-GSM7164801.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 - Liver-28day-rep2-ATAC-GSM7164801.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Liver-180day-rep1-ATAC-GSM7164802.end1.fastq.gz Liver-180day-rep1-ATAC-GSM7164802.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 - Liver-180day-rep1-ATAC-GSM7164802.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Liver-180day-rep2-ATAC-GSM7164803.end1.fastq.gz Liver-180day-rep2-ATAC-GSM7164803.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 - Liver-180day-rep2-ATAC-GSM7164803.2x36mers.noMT.unique