zcat 2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9.50mers.end1.fastq.gz 2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 16 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9.1x50mers.a.e200.offrate1.bam