python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_cerebellum_rep_M22-GSM4799610.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_cerebellum_rep_M22-GSM4799610.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_cerebellum_rep_M22-GSM4799610.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M22-GSM4799614.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M22-GSM4799614.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M22-GSM4799614.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M08-GSM4799617.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M08-GSM4799617.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M08-GSM4799617.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M08-GSM4799621.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M08-GSM4799621.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M08-GSM4799621.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_cerebellum_rep_M22-GSM4799610.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_cerebellum_rep_M22-GSM4799610.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_cerebellum_rep_M22-GSM4799610.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M22-GSM4799614.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M22-GSM4799614.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M22-GSM4799614.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M08-GSM4799617.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M08-GSM4799617.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M08-GSM4799617.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M08-GSM4799621.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M08-GSM4799621.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M08-GSM4799621.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M08-GSM4799625.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M08-GSM4799625.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M08-GSM4799625.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M08-GSM4799629.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M08-GSM4799629.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M08-GSM4799629.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M22-GSM4799630.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M22-GSM4799630.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M22-GSM4799630.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M22-GSM4799607.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M22-GSM4799607.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M22-GSM4799607.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M08-GSM4799625.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M08-GSM4799625.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M08-GSM4799625.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M08-GSM4799629.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M08-GSM4799629.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M08-GSM4799629.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M22-GSM4799630.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M22-GSM4799630.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_skeletal_muscle_rep_M22-GSM4799630.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M22-GSM4799607.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M22-GSM4799607.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M22-GSM4799607.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M08-GSM4799613.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M08-GSM4799613.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M08-GSM4799613.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M22-GSM4799618.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M22-GSM4799618.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M22-GSM4799618.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M22-GSM4799622.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M22-GSM4799622.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M22-GSM4799622.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M08-GSM4799633.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M08-GSM4799633.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M08-GSM4799633.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M08-GSM4799613.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M08-GSM4799613.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_cerebral_cortex_rep_M08-GSM4799613.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M22-GSM4799618.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M22-GSM4799618.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_hypothalamus_rep_M22-GSM4799618.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M22-GSM4799622.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M22-GSM4799622.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_liver_rep_M22-GSM4799622.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M08-GSM4799633.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M08-GSM4799633.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M08-GSM4799633.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M22-GSM4799634.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M22-GSM4799634.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M22-GSM4799634.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M08-GSM4799606.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M08-GSM4799606.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M08-GSM4799606.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M22-GSM4799626.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M22-GSM4799626.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/Bos_taurus-ARS-UCD1.2/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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M22-GSM4799626.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M22-GSM4799634.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M22-GSM4799634.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_spleen_rep_M22-GSM4799634.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M08-GSM4799606.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M08-GSM4799606.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_adipose_rep_M08-GSM4799606.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M22-GSM4799626.end1.fastq.gz ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M22-GSM4799626.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/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.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/Mammals/Bos_taurus-ARS-UCD1.2/bowtie-indexes/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-seq_from_UC_Davis_FAANG_cattle_lung_rep_M22-GSM4799626.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique