zcat DNaseHiC-WG-brain-rep1-GSM1689794/*_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm9/bowtie-indexes/chrM -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm9/bowtie-indexes/mm9.fa - -o DNaseHiC-WG-brain-rep1-GSM1689794.end1.mm9.chrM.v2.unique.bam
zcat insituDNaseHiC-WG-brain-rep1-GSM1689795/*_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm9/bowtie-indexes/chrM -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm9/bowtie-indexes/mm9.fa - -o insituDNaseHiC-WG-brain-rep1-GSM1689795.end1.mm9.chrM.v2.unique.bam
zcat insituDNaseHiC-WG-patski-rep1-GSM1689796/*_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm9/bowtie-indexes/chrM -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm9/bowtie-indexes/mm9.fa - -o insituDNaseHiC-WG-patski-rep1-GSM1689796.end1.mm9.chrM.v2.unique.bam
zcat DNaseHiC-WG-brain-rep1-GSM1689794/*_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm9/bowtie-indexes/chrM -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm9/bowtie-indexes/mm9.fa - -o DNaseHiC-WG-brain-rep1-GSM1689794.end2.mm9.chrM.v2.unique.bam
zcat insituDNaseHiC-WG-brain-rep1-GSM1689795/*_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm9/bowtie-indexes/chrM -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm9/bowtie-indexes/mm9.fa - -o insituDNaseHiC-WG-brain-rep1-GSM1689795.end2.mm9.chrM.v2.unique.bam
zcat insituDNaseHiC-WG-patski-rep1-GSM1689796/*_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm9/bowtie-indexes/chrM -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm9/bowtie-indexes/mm9.fa - -o insituDNaseHiC-WG-patski-rep1-GSM1689796.end2.mm9.chrM.v2.unique.bam