How to do diferential expression analysis of 2 closely related species

How to do diferential expression analysis of 2 closely related species

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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?


Trinity


EdgeR


Diferential-Expression

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