+ --bowtie \
+ --bowtie-path /sw/bowtie \
+ /data/mm9 \
+ /ref/mouse_125
+
+2) Suppose we also want to build Bowtie 2 indices in the above example and Bowtie 2 executables are found in '/sw/bowtie2', the command will be:
+
+ rsem-prepare-reference --gtf mm9.gtf \
+ --transcript-to-gene-map knownIsoforms.txt \
+ --bowtie \