python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC_WT_donor1_Mustela_putorius_furo_ATAC-seq-GSM8208877_r1.end1.fastq.gz ATAC_WT_donor1_Mustela_putorius_furo_ATAC-seq-GSM8208877_r1.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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC -p 8 -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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC_WT_donor1_Mustela_putorius_furo_ATAC-seq-GSM8208877_r1.2x36mers.Mustela_putorius_furo-MusPutFur1.0_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC_WT_donor3_Mustela_putorius_furo_ATAC-seq-GSM8208879_r1.end1.fastq.gz ATAC_WT_donor3_Mustela_putorius_furo_ATAC-seq-GSM8208879_r1.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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC -p 8 -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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC_WT_donor3_Mustela_putorius_furo_ATAC-seq-GSM8208879_r1.2x36mers.Mustela_putorius_furo-MusPutFur1.0_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC_WT_donor2_Mustela_putorius_furo_ATAC-seq-GSM8208878_r1.end1.fastq.gz ATAC_WT_donor2_Mustela_putorius_furo_ATAC-seq-GSM8208878_r1.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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC -p 8 -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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC_WT_donor2_Mustela_putorius_furo_ATAC-seq-GSM8208878_r1.2x36mers.Mustela_putorius_furo-MusPutFur1.0_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC_CFTRKO_knockout_donor3_Mustela_putorius_furo_ATAC-seq-GSM8208876_r1.end1.fastq.gz ATAC_CFTRKO_knockout_donor3_Mustela_putorius_furo_ATAC-seq-GSM8208876_r1.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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC -p 8 -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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC_CFTRKO_knockout_donor3_Mustela_putorius_furo_ATAC-seq-GSM8208876_r1.2x36mers.Mustela_putorius_furo-MusPutFur1.0_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC_CFTRKO_knockout_donor2_Mustela_putorius_furo_ATAC-seq-GSM8208875_r1.end1.fastq.gz ATAC_CFTRKO_knockout_donor2_Mustela_putorius_furo_ATAC-seq-GSM8208875_r1.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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC -p 8 -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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC_CFTRKO_knockout_donor2_Mustela_putorius_furo_ATAC-seq-GSM8208875_r1.2x36mers.Mustela_putorius_furo-MusPutFur1.0_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC_CFTRKO_knockout_donor1_Mustela_putorius_furo_ATAC-seq-GSM8208874_r1.end1.fastq.gz ATAC_CFTRKO_knockout_donor1_Mustela_putorius_furo_ATAC-seq-GSM8208874_r1.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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC -p 8 -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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC_CFTRKO_knockout_donor1_Mustela_putorius_furo_ATAC-seq-GSM8208874_r1.2x36mers.Mustela_putorius_furo-MusPutFur1.0_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC_WT_donor4_Mustela_putorius_furo_ATAC-seq-GSM8208880_r1.end1.fastq.gz ATAC_WT_donor4_Mustela_putorius_furo_ATAC-seq-GSM8208880_r1.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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC -p 8 -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/Mustela_putorius_furo-MusPutFur1.0_HiC-DNAZoo/bowtie-indexes/Mustela_putorius_furo-MusPutFur1.0_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC_WT_donor4_Mustela_putorius_furo_ATAC-seq-GSM8208880_r1.2x36mers.Mustela_putorius_furo-MusPutFur1.0_HiC.unique