How to map metatranscriptomics reads to a given genome (unannotated genome assembly)?

Question

[mrj]

I have a set of metatranscriptomics reads. I would like to map them to a given genome. This genome is not an annotated genome (no GFF file available). It is an unannotated genome assembly. With this kind of data at hand, what is the best way (which tools) to find out if there are transcripts from the given genome available within the metatranscriptomics data?

Answer 1

[Mensur Dlakic]

It is not that difficult to annotate a prokaryotic genome. Really, it can be done in under 10 minutes. A basic way of doing it would be to simply predict genes. Prodigal will do it in under a minute and create a .gff file. If you want to invest a bit more time, prokka will do the annotation and create many useful files, one of which is a .gff file.

[mrj]

Mensur Thank you!!! This solves my problem