zcat R1_mESCs-CTCF-SLIM-ChIP-100U_Mnase-GSM2916417/SRR6453189_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-100U_Mnase-GSM2916417.1x36mers.mm9.unique
zcat R1_mESCs-CTCF-SLIM-ChIP-1.55U_Mnase-GSM2916414/SRR6453186_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-1.55U_Mnase-GSM2916414.1x36mers.mm9.unique
zcat R1_mESCs-CTCF-SLIM-ChIP-_25U_Mnase-GSM2916416/SRR6453188_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-_25U_Mnase-GSM2916416.1x36mers.mm9.unique
zcat R1_mESCs-CTCF-SLIM-ChIP-6.25U_Mnase-GSM2916415/SRR6453187_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-6.25U_Mnase-GSM2916415.1x36mers.mm9.unique
zcat R1_mESCs-CTCF-SLIM-ChIP-Mixed_Mnase-GSM2916418/SRR6453190_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9 -p 8 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-Mixed_Mnase-GSM2916418.1x36mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py R1_mESCs-CTCF-SLIM-ChIP-100U_Mnase-GSM2916417/SRR6453189_1.fastq.gz R1_mESCs-CTCF-SLIM-ChIP-100U_Mnase-GSM2916417/SRR6453189_2.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/mm9/bowtie-indexes/mm9 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-100U_Mnase-GSM2916417.2x36mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py R1_mESCs-CTCF-SLIM-ChIP-1.55U_Mnase-GSM2916414/SRR6453186_1.fastq.gz R1_mESCs-CTCF-SLIM-ChIP-1.55U_Mnase-GSM2916414/SRR6453186_2.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/mm9/bowtie-indexes/mm9 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-1.55U_Mnase-GSM2916414.2x36mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py R1_mESCs-CTCF-SLIM-ChIP-_25U_Mnase-GSM2916416/SRR6453188_1.fastq.gz R1_mESCs-CTCF-SLIM-ChIP-_25U_Mnase-GSM2916416/SRR6453188_2.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/mm9/bowtie-indexes/mm9 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-_25U_Mnase-GSM2916416.2x36mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py R1_mESCs-CTCF-SLIM-ChIP-6.25U_Mnase-GSM2916415/SRR6453187_1.fastq.gz R1_mESCs-CTCF-SLIM-ChIP-6.25U_Mnase-GSM2916415/SRR6453187_2.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/mm9/bowtie-indexes/mm9 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-6.25U_Mnase-GSM2916415.2x36mers.mm9.unique
python ~/code/PEFastqToTabDelimited.py R1_mESCs-CTCF-SLIM-ChIP-Mixed_Mnase-GSM2916418/SRR6453190_1.fastq.gz R1_mESCs-CTCF-SLIM-ChIP-Mixed_Mnase-GSM2916418/SRR6453190_2.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/mm9/bowtie-indexes/mm9 -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 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm9/bowtie-indexes/mm9.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - R1_mESCs-CTCF-SLIM-ChIP-Mixed_Mnase-GSM2916418.2x36mers.mm9.unique