Dear all, I want to compare gene expression of 5 different birds species. For each species, I have RNA-Seq reads from 5 to 10 individuals (single-end Illumina).
My question is what would be the best way to conduct DGE analysis? Should I assemble one transcriptome with all the fastq-files from all species or one transcriptome for each of the species separately?
I am afraid that if I create one big transcriptome, its quality might suffer because not all of the species are very closey related.
Thank you very much, Olaf