python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1334-SSB01-a_amanitin_high-48h-Hi-C/L1334-SSB01-a_amanitin_high-48h-Hi-C____210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1334-SSB01-a_amanitin_high-48h-Hi-C/L1334-SSB01-a_amanitin_high-48h-Hi-C____210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1334-SSB01-a_amanitin_high-48h-Hi-C/L1334-SSB01-a_amanitin_high-48h-Hi-C____210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.210130_NB551514_0540_AHKHVWBGXH.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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 210121L01_exp201015_MS214_SCGE_RAPA-00min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a