python ~/code/PEFastqToTabDelimited.py Cross-contamination-control.SRR6761591_1.fastq.gz Cross-contamination-control.SRR6761591_2.fastq.gz -trim 36 36 -trim5 8 0 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Cross-contamination-control.2x36mers.mm10.unique
python ~/code/PEFastqToTabDelimited.py Mouse-H3K27ac-16-tissues.SRR6761587_1.fastq.gz Mouse-H3K27ac-16-tissues.SRR6761587_2.fastq.gz -trim 36 36 -trim5 8 0 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mouse-H3K27ac-16-tissues.2x36mers.mm10.unique
python ~/code/PEFastqToTabDelimited.py Mouse-H3K27me3-16-tissues.SRR6761589_1.fastq.gz Mouse-H3K27me3-16-tissues.SRR6761589_2.fastq.gz -trim 36 36 -trim5 8 0 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mouse-H3K27me3-16-tissues.2x36mers.mm10.unique
python ~/code/PEFastqToTabDelimited.py Mouse-H3K36me3-16-tissues.SRR6761588_1.fastq.gz Mouse-H3K36me3-16-tissues.SRR6761588_2.fastq.gz -trim 36 36 -trim5 8 0 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mouse-H3K36me3-16-tissues.2x36mers.mm10.unique
python ~/code/PEFastqToTabDelimited.py Mouse-input-16-tissues.SRR6761590_1.fastq.gz Mouse-input-16-tissues.SRR6761590_2.fastq.gz -trim 36 36 -trim5 8 0 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Mouse-input-16-tissues.2x36mers.mm10.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-CTCF-10000.SRR6761517_1.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761518_1.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761519_1.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761520_1.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761521_1.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761522_1.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761523_1.fastq.gz RELACS-HepG2-CTCF-10000.SRR6761517_2.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761518_2.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761519_2.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761520_2.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761521_2.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761522_2.fastq.gz,RELACS-HepG2-CTCF-10000.SRR6761523_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-CTCF-10000.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-CTCF-1000.SRR6761545_1.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761546_1.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761547_1.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761548_1.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761549_1.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761550_1.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761551_1.fastq.gz RELACS-HepG2-CTCF-1000.SRR6761545_2.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761546_2.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761547_2.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761548_2.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761549_2.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761550_2.fastq.gz,RELACS-HepG2-CTCF-1000.SRR6761551_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-CTCF-1000.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-CTCF-100.SRR6761573_1.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761574_1.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761575_1.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761576_1.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761577_1.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761578_1.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761579_1.fastq.gz RELACS-HepG2-CTCF-100.SRR6761573_2.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761574_2.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761575_2.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761576_2.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761577_2.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761578_2.fastq.gz,RELACS-HepG2-CTCF-100.SRR6761579_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-CTCF-100.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-CTCF.SRR6761491_1.fastq.gz RELACS-HepG2-CTCF.SRR6761491_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-CTCF.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K27ac.SRR6761485_1.fastq.gz RELACS-HepG2-H3K27ac.SRR6761485_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K27ac.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K27me3-10000.SRR6761510_1.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761511_1.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761512_1.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761513_1.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761514_1.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761515_1.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761516_1.fastq.gz RELACS-HepG2-H3K27me3-10000.SRR6761510_2.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761511_2.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761512_2.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761513_2.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761514_2.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761515_2.fastq.gz,RELACS-HepG2-H3K27me3-10000.SRR6761516_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K27me3-10000.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K27me3-1000.SRR6761538_1.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761539_1.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761540_1.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761541_1.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761542_1.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761543_1.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761544_1.fastq.gz RELACS-HepG2-H3K27me3-1000.SRR6761538_2.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761539_2.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761540_2.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761541_2.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761542_2.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761543_2.fastq.gz,RELACS-HepG2-H3K27me3-1000.SRR6761544_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K27me3-1000.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K27me3-100.SRR6761566_1.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761567_1.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761568_1.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761569_1.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761570_1.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761571_1.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761572_1.fastq.gz RELACS-HepG2-H3K27me3-100.SRR6761566_2.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761567_2.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761568_2.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761569_2.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761570_2.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761571_2.fastq.gz,RELACS-HepG2-H3K27me3-100.SRR6761572_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K27me3-100.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K27me3.SRR6761490_1.fastq.gz RELACS-HepG2-H3K27me3.SRR6761490_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K27me3.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K36me3.SRR6761488_1.fastq.gz RELACS-HepG2-H3K36me3.SRR6761488_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K36me3.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K4me1.SRR6761487_1.fastq.gz RELACS-HepG2-H3K4me1.SRR6761487_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K4me1.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K4me3-10000.SRR6761503_1.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761504_1.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761505_1.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761506_1.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761507_1.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761508_1.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761509_1.fastq.gz RELACS-HepG2-H3K4me3-10000.SRR6761503_2.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761504_2.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761505_2.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761506_2.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761507_2.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761508_2.fastq.gz,RELACS-HepG2-H3K4me3-10000.SRR6761509_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K4me3-10000.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K4me3-1000.SRR6761531_1.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761532_1.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761533_1.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761534_1.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761535_1.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761536_1.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761537_1.fastq.gz RELACS-HepG2-H3K4me3-1000.SRR6761531_2.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761532_2.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761533_2.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761534_2.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761535_2.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761536_2.fastq.gz,RELACS-HepG2-H3K4me3-1000.SRR6761537_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K4me3-1000.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K4me3-100.SRR6761559_1.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761560_1.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761561_1.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761562_1.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761563_1.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761564_1.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761565_1.fastq.gz RELACS-HepG2-H3K4me3-100.SRR6761559_2.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761560_2.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761561_2.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761562_2.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761563_2.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761564_2.fastq.gz,RELACS-HepG2-H3K4me3-100.SRR6761565_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K4me3-100.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K4me3.SRR6761486_1.fastq.gz RELACS-HepG2-H3K4me3.SRR6761486_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K4me3.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-H3K9me3.SRR6761489_1.fastq.gz RELACS-HepG2-H3K9me3.SRR6761489_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-H3K9me3.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-input-10000.SRR6761524_1.fastq.gz,RELACS-HepG2-input-10000.SRR6761525_1.fastq.gz,RELACS-HepG2-input-10000.SRR6761526_1.fastq.gz,RELACS-HepG2-input-10000.SRR6761527_1.fastq.gz,RELACS-HepG2-input-10000.SRR6761528_1.fastq.gz,RELACS-HepG2-input-10000.SRR6761529_1.fastq.gz,RELACS-HepG2-input-10000.SRR6761530_1.fastq.gz RELACS-HepG2-input-10000.SRR6761524_2.fastq.gz,RELACS-HepG2-input-10000.SRR6761525_2.fastq.gz,RELACS-HepG2-input-10000.SRR6761526_2.fastq.gz,RELACS-HepG2-input-10000.SRR6761527_2.fastq.gz,RELACS-HepG2-input-10000.SRR6761528_2.fastq.gz,RELACS-HepG2-input-10000.SRR6761529_2.fastq.gz,RELACS-HepG2-input-10000.SRR6761530_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-input-10000.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-input-1000.SRR6761552_1.fastq.gz,RELACS-HepG2-input-1000.SRR6761553_1.fastq.gz,RELACS-HepG2-input-1000.SRR6761554_1.fastq.gz,RELACS-HepG2-input-1000.SRR6761555_1.fastq.gz,RELACS-HepG2-input-1000.SRR6761556_1.fastq.gz,RELACS-HepG2-input-1000.SRR6761557_1.fastq.gz,RELACS-HepG2-input-1000.SRR6761558_1.fastq.gz RELACS-HepG2-input-1000.SRR6761552_2.fastq.gz,RELACS-HepG2-input-1000.SRR6761553_2.fastq.gz,RELACS-HepG2-input-1000.SRR6761554_2.fastq.gz,RELACS-HepG2-input-1000.SRR6761555_2.fastq.gz,RELACS-HepG2-input-1000.SRR6761556_2.fastq.gz,RELACS-HepG2-input-1000.SRR6761557_2.fastq.gz,RELACS-HepG2-input-1000.SRR6761558_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-input-1000.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-input-100.SRR6761580_1.fastq.gz,RELACS-HepG2-input-100.SRR6761581_1.fastq.gz,RELACS-HepG2-input-100.SRR6761582_1.fastq.gz,RELACS-HepG2-input-100.SRR6761583_1.fastq.gz,RELACS-HepG2-input-100.SRR6761584_1.fastq.gz,RELACS-HepG2-input-100.SRR6761585_1.fastq.gz,RELACS-HepG2-input-100.SRR6761586_1.fastq.gz RELACS-HepG2-input-100.SRR6761580_2.fastq.gz,RELACS-HepG2-input-100.SRR6761581_2.fastq.gz,RELACS-HepG2-input-100.SRR6761582_2.fastq.gz,RELACS-HepG2-input-100.SRR6761583_2.fastq.gz,RELACS-HepG2-input-100.SRR6761584_2.fastq.gz,RELACS-HepG2-input-100.SRR6761585_2.fastq.gz,RELACS-HepG2-input-100.SRR6761586_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-input-100.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-input.SRR6761493_1.fastq.gz RELACS-HepG2-input.SRR6761493_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-input.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py RELACS-HepG2-p300.SRR6761492_1.fastq.gz RELACS-HepG2-p300.SRR6761492_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - RELACS-HepG2-p300.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py Traditional-HepG2-CTCF.SRR6761500_1.fastq.gz Traditional-HepG2-CTCF.SRR6761500_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - Traditional-HepG2-CTCF.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py Traditional-HepG2-H3K27ac.SRR6761494_1.fastq.gz Traditional-HepG2-H3K27ac.SRR6761494_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - Traditional-HepG2-H3K27ac.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py Traditional-HepG2-H3K27me3.SRR6761499_1.fastq.gz Traditional-HepG2-H3K27me3.SRR6761499_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - Traditional-HepG2-H3K27me3.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py Traditional-HepG2-H3K36me3.SRR6761497_1.fastq.gz Traditional-HepG2-H3K36me3.SRR6761497_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - Traditional-HepG2-H3K36me3.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py TraditionalHepG2-H3K4me1.SRR6761496_1.fastq.gz TraditionalHepG2-H3K4me1.SRR6761496_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - TraditionalHepG2-H3K4me1.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py Traditional-HepG2-H3K4me3.SRR6761495_1.fastq.gz Traditional-HepG2-H3K4me3.SRR6761495_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - Traditional-HepG2-H3K4me3.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py Traditional-HepG2-H3K9me3.SRR6761498_1.fastq.gz Traditional-HepG2-H3K9me3.SRR6761498_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - Traditional-HepG2-H3K9me3.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py Traditional-HepG2-input.SRR6761502_1.fastq.gz Traditional-HepG2-input.SRR6761502_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - Traditional-HepG2-input.2x36mers.hg38-male.unique
python ~/code/PEFastqToTabDelimited.py Traditional-HepG2-p300.SRR6761501_1.fastq.gz Traditional-HepG2-p300.SRR6761501_2.fastq.gz -trim 36 36 -trim5 8 0 | /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 -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 - Traditional-HepG2-p300.2x36mers.hg38-male.unique