#!/bin/bash

GENOME=$1
VERSION=$2
/project/umw_biocore/bin/RSEM/rsem-prepare-reference --bowtie-path /project/umw_biocore/bin/bowtie-0.12.9 --gtf /share/data/umw_biocore/genome_data/$GENOME/$VERSION/ucsc.gtf --transcript-to-gene-map /share/data/umw_biocore/genome_data/$GENOME/$VERSION/ucsc_into_genesymbol.rsem /share/data/umw_biocore/genome_data/$GENOME/$VERSION/$VERSION.fa /share/data/umw_biocore/genome_data/$GENOME/$VERSION/rsem_ref
