I want to try to do a population study. I am working on an organism that cannot be cultured. That's why I used metagenomic data.
I haven't managed to get the genome of this organism because it's too complicated to extract the genome from metaG data. But I did manage to get the transcriptome of this organism because I think I managed to extract this transcriptome from the metaT data.
I did polyA RNA library prep to have eukaryotic RNA.
I thought that, based on this transcriptome, it might be possible to carry out my population study:
I'm going to map my metaG reads onto the metaT data.
I know that my species is the main species of the clade, so most of the time, if there's a match with my database, I know it must be my species.
I can then do my variant study to do my population study.
But I don't know if it's possible or not, or if it's rigorous enough, because in the metaG data there are introns and non-coding DNA, so I think it can create a problem for the mapping step. What's more, we usually do the opposite: we map Transcriptomic data onto genomic data, so my method is unusual. What do you think of this idea?