What Annotation file should be used for EdgeR?

Hi! I’m doing an RNAseq analysis. Do you know if it’s correct to use an annotation file normalized with DESeq2 (and annotated with Annotate DESeq2/DEXSeq output tables) in limma-voom or EdgeR? Since they use different normalization methods, I’m not sure if it will affect my results.
Do you think it would be enough to turn off the normalization option in EdgeR, so it doesn’t get normalized twice? Or what tool would you recommend to get a differential expression table if I want to use EdgeR? I’ve seen in tutorials that AnnotateMyIDs is useful, but I’m not working with any of the organisms it can be used for.
I hope you can help! Thanks!

Hi MarioG

For edgeR you need a count table with the raw read counts (i.e. not normalized data), See chapter 2.3 in the edgeR users guide (https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf)

Regards, Hans-Rudolf

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