GO analysis without gene IDs?
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@bahmanikmsuedu-23146
Last seen 19 months ago
Michigan State University

Hi. I work on a plant, which doesn't have reference genome. I performed a RNA seq experiment (using a transcriptome), and then using DESeq2 I found differentially expressed genes (DEGs). I thought GO analysis is going to be my next step, but I don't have the gene IDs, and I cant get them (I think nothing else other than gene IDs is acceptable as input for GO analysis). I only have the transcript names which are like 200 letters long (here is one of the transcript names as an example: "Locus13219Transcript2/2Confidence0.714Length716;heatshockcognate70kDaprotein-like[Helianthusannuus]&gtref|XP022034086.1|putativeheatshockprotein70familypeptide-bindingdomainprotein[Helianthusannuus]XP022034085;nr"). Now that I have the DEGs, what is the next step for me? Thank you,

deseq2 annotation go • 217 views
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@mikelove
Last seen 1 day ago
United States

Check out the goseq documentation which has guides for gene set enrichment for various organisms.

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I will check that out, thank you

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