Homolog-level DGE analyses - what to consider?
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3.3 years ago
ponganta ▴ 590


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:

  1. de novo assembly of transcripts
  2. annotation
  3. quantification (Salmon)
  4. Count aggregation on a homolog level (tximport)
  5. 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!

RNA-Seq Differential-Gene-Expression DESeq2 • 615 views

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