I'm currently working on tissue-specific RNAseq data of a non-model polyploid, which is however closely related to a model species. My goal is to identify tissue-specific DEGs via pairwise comparisons.
I approached this task by:
- de novo assembly of transcripts
- quantification (Salmon)
- Count aggregation on a homolog level (tximport)
- Determining tissue-specific DEGs (using DESeq2::DESeq and DESeq2::lfcShrink)
My question is:
Does anyone have remarks on what is to be considered when dealing with homolog-level DGE analysis? Any pitfalls to watch out for? Transcriptome assembly and annotation are, as far as I can tell, of fairly high quality (transrate score: 0.4, mean bitscore: 640).
I'd be thankful for any insights!