I'm doing a DE analysis using deseq2 with a non-model species, thus I retrieved annotation using biomaRt in R. I've imported kallisto counts using tximport and collapsing transcripts to genes (txOut=FALSE). I collapsed transcripts either to "Ensembl gene ID" or to "external gene name" and I got a slighly different output in term of DE genes. I suppose this is due to the fact that if you collapse to gene names you lose all the genes without a definite gene name. This, in turn, affects the total number of genes considered and the FDR calculations. Isn't it?
Said that, in your opinion which is the best option? using gene IDs or gene names?
Thanks in advance for you help!