zcat CH12-ENCSR005UON-ENCLB181IOP.end1.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 CH12-ENCSR005UON-ENCLB181IOP.end1.mm9.chrM.v2.unique.bam
zcat CH12-ENCSR005UON-ENCLB181IOP.end2.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 CH12-ENCSR005UON-ENCLB181IOP.end2.mm9.chrM.v2.unique.bam