python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py OmniATAC-seq_Horse_HoMel-L1_BL-GSM4223587.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Equus_caballus.EquCab2/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Equus_caballus.EquCab2/bowtie-indexes/Equus_caballus.EquCab2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OmniATAC-seq_Horse_HoMel-L1_BL-GSM4223587.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py OmniATAC-seq_Horse_HoMel-A1_BL-GSM4223588.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Equus_caballus.EquCab2/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Equus_caballus.EquCab2/bowtie-indexes/Equus_caballus.EquCab2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OmniATAC-seq_Horse_HoMel-A1_BL-GSM4223588.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py OmniATAC-seq_Horse_HoMel-L1_BL-GSM4223587.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Equus_caballus.EquCab2/bowtie-indexes/Equus_caballus.EquCab2.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | 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/Equus_caballus.EquCab2/bowtie-indexes/Equus_caballus.EquCab2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OmniATAC-seq_Horse_HoMel-L1_BL-GSM4223587.1x36mers.Equus_caballus.EquCab2.dna.toplevel.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py OmniATAC-seq_Horse_HoMel-A1_BL-GSM4223588.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Equus_caballus.EquCab2/bowtie-indexes/Equus_caballus.EquCab2.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | 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/Equus_caballus.EquCab2/bowtie-indexes/Equus_caballus.EquCab2.dna.toplevel.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OmniATAC-seq_Horse_HoMel-A1_BL-GSM4223588.1x36mers.Equus_caballus.EquCab2.dna.toplevel.unique