export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o Cas13-sgRNAs.____final_set.no-rRNA.finalized-TopHat-2.0.8-GENCODEv25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male Cas13-sgRNAs.____final_set.no-rRNA.finalized.fa