python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_010.end1.fastq.gz 18hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_010.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_010.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_015.end1.fastq.gz 18hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_015.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_015.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_010.end1.fastq.gz 18hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_010.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_010.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_015.end1.fastq.gz 18hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_015.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_015.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_017.end1.fastq.gz 24hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_017.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_017.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_016.end1.fastq.gz 18hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_016.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_016.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_017.end1.fastq.gz 24hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_017.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24hr_Mock_infected_ATAC-seq_Bio_rep_1-2803_017.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_016.end1.fastq.gz 18hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_016.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_016.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_009.end1.fastq.gz 18hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_009.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_009.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 12hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_008.end1.fastq.gz 12hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_008.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 12hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_008.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 12hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_014.end1.fastq.gz 12hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_014.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 12hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_014.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_018.end1.fastq.gz 24hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_018.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_018.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_009.end1.fastq.gz 18hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_009.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_009.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 12hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_008.end1.fastq.gz 12hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_008.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 12hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_008.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 12hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_014.end1.fastq.gz 12hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_014.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 12hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_014.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_018.end1.fastq.gz 24hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_018.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24hr_MVA_infected_ATAC-seq_Bio_rep_1-2803_018.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_012.end1.fastq.gz 24hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_012.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_012.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 12hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_007.end1.fastq.gz 12hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_007.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 12hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_007.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_011.end1.fastq.gz 24hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_011.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/chrM -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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_011.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_012.end1.fastq.gz 24hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_012.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24hr_MVA_infected_ATAC-seq_Bio_rep_2-2803_012.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 12hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_007.end1.fastq.gz 12hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_007.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 12hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_007.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_011.end1.fastq.gz 24hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_011.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/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24hr_Mock_infected_ATAC-seq_Bio_rep_2-2803_011.2x36mers.Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.unique