python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4901-HEK_GFP_1_MNase.251204_NB551514_0387_AH2KGNBGY2.end1.fastq.gz L4901-HEK_GFP_1_MNase.251204_NB551514_0387_AH2KGNBGY2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -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/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4901-HEK_GFP_1_MNase.2x36mers.unique