GSEA following RNAseq experiment when don't have a sequenced genome?

Question

[pterry]

Can one do GSEA following RNAseq experiment when don't have a sequenced genome for the experimental organism? The alignment of RNAseq reads is done against the transcriptome of the experimental organism. Thus no gene annotation for the rows of the counts table. Of course, normally would have gene annotation for each row of counts table when proceed to GSEA analysis following RNAseq differential expression.

Answer 1

[Sean Davis]

GSEA is Gene Set Enrichment Analysis, so you need to have some way to assign your genes to sets that are of interest to you. If you cannot do that, then GSEA will not be terribly relevant for you.

If you need help assigning your genes to gene sets, then you'll need to edit your question with more detail.