Is it ok to map RNA-seq reads on prokaryotic reference genome with bowtie2 ?

Question

[liuyifan2014]

Hi everyone, it is usually recommend to use TopHat to map reads on reference genome due to intron's reason. However there is no intron in prokaryotes.

So I would like to know if it is ok to use bowtie2 instead of TopHap under this condition?

Best

[h.mon]

It is probably even better to use HISAT2:

HISAT2 is a successor to both HISAT and TopHat2. We recommend that the HISAT and TopHat2 users switch to HISAT2. 

[User 59]

HISAT, HISAT2, and TopHat2 are splice aware aligners. The OP is not interested in splicing-aware aligners, hence the question being about bowtie2 and not Tophat, which he has rightly eliminated as being inappropriate already..

[h.mon]

It probably wouldn't make much of a difference on the final result.

Anyway, from HISAT2 site:

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) [...]

Answer 1

[mark.ziemann]

It's OK to use bowtie2. However if this is something you will be doing a lot, then it would be good to have a comparison of both methods.