python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BNC_D4_1_ATACseq.end1.fastq.gz BNC_D4_1_ATACseq.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 - BNC_D4_1_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BNC_D4_2_ATACseq.end1.fastq.gz BNC_D4_2_ATACseq.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 - BNC_D4_2_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BNC_D4_3_ATACseq.end1.fastq.gz BNC_D4_3_ATACseq.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 - BNC_D4_3_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bTSC_1_ATACseq.end1.fastq.gz bTSC_1_ATACseq.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 - bTSC_1_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BNC_D4_1_ATACseq.end1.fastq.gz BNC_D4_1_ATACseq.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 - BNC_D4_1_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BNC_D4_2_ATACseq.end1.fastq.gz BNC_D4_2_ATACseq.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 - BNC_D4_2_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BNC_D4_3_ATACseq.end1.fastq.gz BNC_D4_3_ATACseq.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 - BNC_D4_3_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bTSC_1_ATACseq.end1.fastq.gz bTSC_1_ATACseq.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 - bTSC_1_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bTSC_2_ATACseq.end1.fastq.gz bTSC_2_ATACseq.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 - bTSC_2_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bTSC_3_ATACseq.end1.fastq.gz bTSC_3_ATACseq.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 - bTSC_3_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D14_TE_1_ATACseq.end1.fastq.gz D14_TE_1_ATACseq.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 - D14_TE_1_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D14_TE_2_ATACseq.end1.fastq.gz D14_TE_2_ATACseq.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 - D14_TE_2_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bTSC_2_ATACseq.end1.fastq.gz bTSC_2_ATACseq.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 - bTSC_2_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bTSC_3_ATACseq.end1.fastq.gz bTSC_3_ATACseq.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 - bTSC_3_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D14_TE_1_ATACseq.end1.fastq.gz D14_TE_1_ATACseq.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 - D14_TE_1_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D14_TE_2_ATACseq.end1.fastq.gz D14_TE_2_ATACseq.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 - D14_TE_2_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D14_TE_3_ATACseq.end1.fastq.gz D14_TE_3_ATACseq.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 - D14_TE_3_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D7_TE_1_ATACseq.end1.fastq.gz D7_TE_1_ATACseq.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 - D7_TE_1_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D7_TE_2_ATACseq.end1.fastq.gz D7_TE_2_ATACseq.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 - D7_TE_2_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D7_TE_3_ATACseq.end1.fastq.gz D7_TE_3_ATACseq.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 - D7_TE_3_ATACseq.2x36mers.MT python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D14_TE_3_ATACseq.end1.fastq.gz D14_TE_3_ATACseq.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 - D14_TE_3_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D7_TE_1_ATACseq.end1.fastq.gz D7_TE_1_ATACseq.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 - D7_TE_1_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D7_TE_2_ATACseq.end1.fastq.gz D7_TE_2_ATACseq.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 - D7_TE_2_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py D7_TE_3_ATACseq.end1.fastq.gz D7_TE_3_ATACseq.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 - D7_TE_3_ATACseq.2x36mers.Bos_taurus.ARS-UCD1.2.dna.toplevel.unique