How to perform KEGG enrichment analysis for DE genes from a de-novo transcriptome?

Question

[Raito92]

Hello, I'm running a pipeline to analyze differential expression for transcripts predicted and BLAST-annotated from a de-novo assembled transcriptome... At the end of the pipeline, I'm interested in a KEGG Enrichment analysis, but I have no idea about how to perform it. I used Trinity till now but no functions for this kind of analysis are supported, so I guess I need an external script. But I was unable to find a reliable strategy to perform it with external functions.

More specifically, most functions are designed to work for a specific organism, when my transcripts are annotated against a lot of species...

Any suggestions?Thanks in advance!

Answer 1

[GenoMax]

when my transcripts are annotated against a lot of species...

Transcripts should be annotated for function not other species. Sure the "hits" from blast searches or whatever you may have done are to other species but based on the homology you need to decide if the sequence codes for the particular gene it seems to be pointing to.

I believe GeneSCF v.1.0 is able to use custom databases. Take a look to see if it will work in your case.

[Raito92]

It worked like a bless! Thank you!