Dear all,
I am working on three (close) non model species without reference genome. After RNAseq, i assembled the reads (Trinity) and then clustered the contigs (Corset). This has been done independently for each of the three species. Now, I would like to retrieve the homologous clusters between the three species. I tried to perform reciprocal blastn (species1-species2/species2-species1; species2-species3/species3-species2; species1-species3/species3-species1), which gave interesting results, but I read it is not always the best way to proceed. I also predicted the protein using TransDecoder and used the results as input for OrthoFinder. However, cluster without predicted protein (i.e non-coding RNA) are not considered. Could you advice me about the better way to follow among the numerous different possibilities ?
Thank you in advance,
Jean
