Hello all, currently I'm working on the de novo assembly of a non-model plant. I've got tissue-specific illumina-, as well as whole-plant ONP-cDNA-reads. My current plans are as follows:
- Conducting master-assemblies (short read & Hybrid) using the three best assemblers out there (Trinity, transabyss, rnaspades, according to Hölzer & Marz 2019)
- Merging these assemblies
- Assembly evaluation (Busco, Transrate, Salmon)
- Analysis of DEG
Regarding the merging of transcriptomes I've got a few questions: I'd like to build supertranscripts using Corset & Lace (Davidson et al. 2017). How does one go about annotating these for later differential expression analysis?
How do you analyse the quality of supertranscripts?
Are other merging techniques better suited? (There are alternative approaches, namely selecting longest sequence per assembled transcript, longest coding region, or by shared alignment [Gilbert 2019, Davidson et al. 2014])
If anyone has some insights into this, I'd be very thankful.
Edit: changed "differential expression" to "differential expression analysis"