Hello everyone.
I am trying to do differential expression analysis between two different fish species. They are the same genus, and diverged approximately 3 MYA.
I have two different tissues sequenced in each species: eyes and skin.
Therefore my samples are as follows:
Eyes samples:
Species 1 replicate 1
Species 1 replicate 2
Species 1 replicate 3
Species 2 replicate 1
Species 2 replicate 2
Species 2 replicate 3
And the same structure with the Skin samples.
I have used trinity two mount two de novo transcriptomes, one of each tissue, but now I think that this is conceptually wrong because i can create hybrid transcripts between species.
So my main idea now is to make one trinity assembly for each species and each tissue. Then i would somehow extract only the orthologs sequences between species for each tissue. And at last I would do differential expression analysis between species with only the orthologs sequences.
But i am not completely sure if this is right, and what is the best approach to do so. Will I be abble to do differential expression between two trinity assemblies?
Has anyone tried an approach like this before?
