RNA-seq for mixed population

[kavican]

I have the same problem. the thing was to first map the reads from 16S rRNA database and pick the strains that is mapped. Then, you select the bacterial genomes on your second mapping.

I wonder if you slove your problem?

[phdveg]

Has anyone had experience using RNA-seq to distinguish species in a mixed culture? If so did you map transcripts from the sample to two different reference genomes or handle analysis in another method?

Thanks in advance.