/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-prepare-reference --star --star-path /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a -bowtie2 --bowtie2-path /oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0 --bowtie --bowtie-path /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch --gtf stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa stringtie1.3.3b.PolyA+Total-with_annotation.merge