python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py K562-UW-DNAse-ENCLB253REF.end1.36mers.fastq.gz K562-UW-DNAse-ENCLB253REF.end2.36mers.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/hg19/bowtie-indexes/hg19-female -p 16 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-1.1/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-1.1/samtools sort - K562-UW-DNAse-ENCLB253REF.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py K562-UW-DNAse-ENCLB843GMH.end1.36mers.fastq.gz K562-UW-DNAse-ENCLB843GMH.end2.36mers.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/hg19/bowtie-indexes/hg19-female -p 16 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-1.1/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-1.1/samtools sort - K562-UW-DNAse-ENCLB843GMH.2x36mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py K562-UW-DNAse-ENCLB540ZZZ.27mers.fastq.gz 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 16 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-1.1/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-1.1/samtools sort - K562-UW-DNAse-ENCLB540ZZZ.1x25mers.unique