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

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

rna-seq alignment genome
• 3,933 views • link
updated by mark.ziemann mark.ziemann • written by liuyifan2014 • liuyifan2014

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.
• 1 views • link
written by h.mon h.mon

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..

• 0 views • link
written by User 59 User 59

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) [...]
• 0 views • link
written by h.mon h.mon

1 answer

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.

• 1 views • link
written by mark.ziemann mark.ziemann

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