zcat DNaseHiC-WG-H1-GSM1370433/*_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/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/hg19/bowtie-indexes/hg19.fa - -o DNaseHiC-WG-H1-GSM1370433.end1.hg19.chrM.v2.unique.bam
zcat DNaseHiC-WG-K562-GSM1370434/*_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/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/hg19/bowtie-indexes/hg19.fa - -o DNaseHiC-WG-K562-GSM1370434.end1.hg19.chrM.v2.unique.bam
zcat DNaseHiC-WG-H1-GSM1370433/*_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/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/hg19/bowtie-indexes/hg19.fa - -o DNaseHiC-WG-H1-GSM1370433.end2.hg19.chrM.v2.unique.bam
zcat DNaseHiC-WG-K562-GSM1370434/*_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/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/hg19/bowtie-indexes/hg19.fa - -o DNaseHiC-WG-K562-GSM1370434.end2.hg19.chrM.v2.unique.bam