python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Kidney_ATAC1-GSM4818101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Kidney_ATAC1-GSM4818101.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Kidney_ATAC1-GSM4818101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Kidney_ATAC1-GSM4818101.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BMDM1hKLA_ATAC1-GSM4818094.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BMDM1hKLA_ATAC1-GSM4818094.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BMDMwt_ATAC2-GSM4818097.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BMDMwt_ATAC2-GSM4818097.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BMDM1hKLA_ATAC1-GSM4818094.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BMDM1hKLA_ATAC1-GSM4818094.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BMDMwt_ATAC2-GSM4818097.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BMDMwt_ATAC2-GSM4818097.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Liver_ATAC1-GSM4818102.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Liver_ATAC1-GSM4818102.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Lung_ATAC1-GSM4818103.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Lung_ATAC1-GSM4818103.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Spleen_ATAC1-GSM4818104.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Spleen_ATAC1-GSM4818104.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BMDMwt_ATAC1-GSM4818096.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BMDMwt_ATAC1-GSM4818096.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Liver_ATAC1-GSM4818102.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Liver_ATAC1-GSM4818102.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Lung_ATAC1-GSM4818103.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Lung_ATAC1-GSM4818103.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Spleen_ATAC1-GSM4818104.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Spleen_ATAC1-GSM4818104.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py BMDMwt_ATAC1-GSM4818096.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BMDMwt_ATAC1-GSM4818096.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Brain_ATAC1-GSM4818098.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Brain_ATAC1-GSM4818098.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CHO_ATAC3-GSM4818100.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - CHO_ATAC3-GSM4818100.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CHO_ATAC1-GSM4818099.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/chrM -p 8 -v 2 -a -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/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - CHO_ATAC1-GSM4818099.1x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Brain_ATAC1-GSM4818098.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Brain_ATAC1-GSM4818098.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CHO_ATAC3-GSM4818100.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - CHO_ATAC3-GSM4818100.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py CHO_ATAC1-GSM4818099.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cricetulus_griseus-CriGri-PICR_HiC/bowtie-indexes/Cricetulus_griseus-CriGri-PICR_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - CHO_ATAC1-GSM4818099.1x36mers.Cricetulus_griseus-CriGri-PICR_HiC.unique