+transcripts using the Bowtie alignment program. Turn on '--bowtie2'
+for 'rsem-prepare-reference' and 'rsem-calculate-expression' will
+allow RSEM to use the Bowtie 2 alignment program instead. Please note
+that indel alignments, local alignments and discordant alignments are
+disallowed when RSEM uses Bowtie 2 since RSEM currently cannot handle
+them. See the description of '--bowtie2' option in
+'rsem-calculate-expression' for more details. To use an alternative