I've been having a lot of problems using bowtie in conjunction with eXpress (http://bio.math.berkeley.edu/eXpress/tutorial.html) to align and count RNA-seq reads. I decided to try to use bowtie2 instead, and I built my bowtie2 index using bowtie2 2.2.5's bowtie-build command with the option '-o 1' in order to index with an offrate of 1, and this worked just fine.
When I try to use these indices in an alignment with the '-o 1' option, I get this error message:
invalid option -- 'o'
And looking to the help page that comes along with the error, offrate is not, in fact, an option in bowtie2:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share
whereas the bowtie2 manual online states that it is an option:
Override the offrate of the index with
I have tried using bowtie2 2.2.5, the newest version, and bowtie2 2.2.4, but neither seem to have --offrate as an input option for alignment. Am I missing something? Do I need a different version of the program? Any thoughts would be appreciated.