python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P348-GSM4799608.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P348-GSM4799608.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 - ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P348-GSM4799608.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P350-GSM4799609.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P350-GSM4799609.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 - ATAC-seq_from_UC_Davis_FAANG_pig_adipose_rep_P350-GSM4799609.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P348-GSM4799611.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P348-GSM4799611.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 - ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P348-GSM4799611.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P350-GSM4799612.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P350-GSM4799612.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 - ATAC-seq_from_UC_Davis_FAANG_pig_cerebellum_rep_P350-GSM4799612.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P348-GSM4799615.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P348-GSM4799615.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 - ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P348-GSM4799615.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P350-GSM4799616.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P350-GSM4799616.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 - ATAC-seq_from_UC_Davis_FAANG_pig_cerebral_cortex_rep_P350-GSM4799616.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P348-GSM4799619.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P348-GSM4799619.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 - ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P348-GSM4799619.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P350-GSM4799620.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P350-GSM4799620.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 - ATAC-seq_from_UC_Davis_FAANG_pig_hypothalamus_rep_P350-GSM4799620.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P348-GSM4799623.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P348-GSM4799623.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 - ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P348-GSM4799623.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P350-GSM4799624.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P350-GSM4799624.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 - ATAC-seq_from_UC_Davis_FAANG_pig_liver_rep_P350-GSM4799624.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P348-GSM4799627.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P348-GSM4799627.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 - ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P348-GSM4799627.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P350-GSM4799628.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P350-GSM4799628.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 - ATAC-seq_from_UC_Davis_FAANG_pig_lung_rep_P350-GSM4799628.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P348-GSM4799631.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P348-GSM4799631.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 - ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P348-GSM4799631.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P350-GSM4799632.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P350-GSM4799632.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 - ATAC-seq_from_UC_Davis_FAANG_pig_skeletal_muscle_rep_P350-GSM4799632.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P348-GSM4799635.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P348-GSM4799635.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 - ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P348-GSM4799635.2x36mers.noMT.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P350-GSM4799636.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P350-GSM4799636.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 - ATAC-seq_from_UC_Davis_FAANG_pig_spleen_rep_P350-GSM4799636.2x36mers.noMT.unique