Hello all
I have used Trinity to assemble my RNAseq data (non-model species with no genome available), for subsequent DE analysis. I happen to have access to a complete transcriptome from the same species (but not access to the raw data), and I was thinking abut combining both into a (probably better?) reference transcriptome to run my DE analyses, and see whether the results differ and/or improve between both strategies.
I wonder what is the best strategy to do this. It may be possible to get access to the raw data for the additional transcriptome and run Trinity with all the data, but in case I cannot get the data, I would need to use a different approach.
Any advice on this would be really appreciated
Thanks in advance
Olalla
I have used Trinity to assemble my RNAseq data (non-model species with no genome available), for subsequent DE analysis. I happen to have access to a complete transcriptome from the same species (but not access to the raw data), and I was thinking abut combining both into a (probably better?) reference transcriptome to run my DE analyses, and see whether the results differ and/or improve between both strategies.
I wonder what is the best strategy to do this. It may be possible to get access to the raw data for the additional transcriptome and run Trinity with all the data, but in case I cannot get the data, I would need to use a different approach.
Any advice on this would be really appreciated
Thanks in advance
Olalla