I am trying to generate single nuclei RNA seq libraries from a non-model organism. We have a genome that it is not well annotated and a bit incomplete. I know that for single cell RNA seq is possible to do the bioinformatics analyses with an assembled transcriptome but not sure whether is the same case for single nuclei RNA seq.
Susanta Roy
If the genome is incomplete or poorly annotated, a transcriptome-based analysis using a custom-assembled transcriptome is preferred. Hybrid approaches that combine information from both genome and transcriptome data may be considered.
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