Hello Community, after creating a gene transcripts per sample table from my RNASeq reads dataset from a low characterized plant species, I have performed a differential expressed genes analysis using DESeq2. The problem is I have a lot of differentally expressed genes with no functional annotations. I have used eggnogmapper to annotate the transcripts, so regarding this, What can I do in this sense? My goal is to produce a figure of the DEGs across my conditions, but if I have loosing annotations for some relevant genes I'm missing important data that I dont want to miss in the graphs. So, should I test another annotation tool? if so, which would you recommend? or should I only report those genes with annotations and exclude all those DEGs that has no functional annotation?
It will be a bad idea to discard all those DEGs that were not annotated with eggnogmapper so I will appreciate your opinions on this.
I ran eggnogmapper in the following way;
emapper.py -m diamond --itype CDS -i FASTA_FILE_NTS -o test
bests,
Valentín.
What do you mean by "low characterized plant species"? How many gene predictions does it have?
There are a few options I see: