RNA-seq analysis with contigs instead of an assembled genome

Question

[langziv]

Hello

How can one do such analysis without assembling the genome? Is it possible?

[biofalconch]

Yes, it is possible and there are a few was to go and tackle the problem. The one that might be most convenient for you is doing a de-novo transcriptome assembly. There are a few programs that can do this:

• Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
• RNASpades: https://cab.spbu.ru/software/rnaspades/

Answer 1

[dthorbur]

Yes, you most certainly can do this analysis. Contig-level assemblies may have more duplicated genes not collapsed into a single locus, but otherwise should be fine. If the assembly was released in a study, you can check how complete the transcriptome is estimated to be.

You can do one of these analyses following any of the numerous tutorials available online.