RNA-seq analysis with contigs instead of an assembled genome
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13 months ago
langziv ▴ 70

Hello

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

rna-seq • 764 views
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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:

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13 months ago
dthorbur ★ 2.5k

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.

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