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