python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1/L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1.221115_A00509_0639_AHJWLCDSX5.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1/L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1.230114_NB551514_0006_AH7WM5BGXN.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1/L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1.221115_A00509_0639_AHJWLCDSX5.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-ATAC/L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1/L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1.230114_NB551514_0006_AH7WM5BGXN.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/Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/bowtie-indexes/Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC -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/Metazoa/Mammals/Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/bowtie-indexes/Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L2406-Urocyon_littoralis-Island_fox-Sample4508-rep1.2x36mers.ASM813125v1_HiC.unique