Hi, I am willing to try to perform a kind of differential analysis using DESeq2 among two groups of different species (same genus).
I read what was posted previously in this link but unfortunately I cannot reply that workflow since there is only one genome available so that I have to map everything against it. Problem is the systematic bias I create, given (also) that the two groups have different mapping rates, with one with higher similarity to the sequenced genome than the other group.
I am aware that such approach is quite 'unadviceable' but still if anyone believes there is a way to do it, it would be very appreciated ^_^
Since I assembled the RNAseq reads using Trinity, maybe I could use with that the approach used in the post above with some modifications: given the redundancy in Trinity maybe I could use the Supertranscripts and recognize the supposed orthologs based on Blast reciprocal best hit? I do not think that just lowering the mapping stringency would help.
Many thanks for your advices!
