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
Hi Olaf
I am also working on cross-species transcriptomics for my PhD. How is it going , did you figure out the pipeline? I don't have genomes so first I made de novo assemblies using Trinity and determined the expression level of each transcript. Currently I am working on defining my single-copy orthologues between different species pairs using Orthofinder. I guess that should be the starting point.
Also, there is a new normalisation method called SCBN useful for this kind of analysis, I plan to test it on my data. https://pubmed.ncbi.nlm.nih.gov/30925894/
Best,
Lada