Bowtie2 offrate option?

Question

[ols5fg]

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:

 Performance:
  -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: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line-2

Performance options

-o/--offrate <int>

Override the offrate of the index with <int>. If <int> is greater than the offrate used to build the index, then some row markings are discarded when the index is read into memory. This reduces the memory footprint of the aligner but requires more time to calculate text offsets. <int> must be greater than the value used to build the index.

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.

[h.mon]

The manual says you must call -o with a value greater than the one used to build the index, but you are calling it with the same value. Did you try to use a larger value?

[ols5fg]

Thank you for your reply, however even with a higher <int> with the -o or --offrate option, the program returns that 'o' is an invalid option.

[Devon Ryan]

I'm not entirely sure that that option ever actually existed.

Answer 1

[PS]

It's an option for bowtie2-build, to be used when building the index. bowtie2-build documentation.