I am using Trinity from last couple-up months or so. Initially, using same species in different condition was worked fine for me. Now i am trying to do a DE analysis using multiple species. Actually, i have 3 fish performs similar behaviour and another 3 performs similar strategy. Here i considered 3 similar species as replicate for one type (and totally i have two type) . Though these are 6 different species but belong to same family.
I have already made a combine assembly according to trinity protocol (--samples_file). After assembly i have checked the separate alignment rate for each species and it was above 85%. And lastly i checked heat-map and it gave me a result that somehow match with my expectation.
But i am a bit confused about the possible generation of "assembly chimera". In most of the cases i found people do DE analysis with same species. Also didn't find any reference article that did multiple species DE analysis using Trinity pipeline. So it will be a great help for me if i get some suggestion that either i should go with existing result or i need to find another way.