I have paired end reads using target capture approach for 300 samples on 40,000 conserved regions/baits. I look at the baits and flanking for variable sites to reconstruct trees. The baits were designed on intronic and genic regions both.
Does anyone know how to ensure I only look at orthologs and remove paralogs from my dataset? I saw papers using OrthoFinder, HybPiper and MCScan but these are software for only CDS.
I would suspect that the intronic regions will be too variable to be aligned well, regardless of paralogy, although perhaps in some systems this is not true? If you are baiting them I suppose there is evidence that they will have information, and orthologous genes should have more conserved introns. . .If you have baited intronic and exonic regions from the same genes, and can associate them, then of course you can do orthology prediction on just the coding sequence and those results will tell you about the introns as well.
- Badges
- Science topic