Hi all Annotation Experts out there,
Currently, I am working with differential gene expression in a non-model organism. For this, I have used Kallisto/Sleuth and is very pleased with the process as well as the results.
But I am stuck and would be really grateful for some help to move on.
My issue is getting gene names into Sleuth instead of the Trinity "gene" names (for heat maps etc.). I have done an annotation of my de novo reference transcriptome (assembled with Trinity) in Diamond, which results in a .m8 file with accession numbers.
My questions are: 1) how do I obtain gene names instead of accession numbers? 2) how do I get my annotation with gene names into Sleuth? The examples I have seen is using ESEMBL and "pre-made" annotations from fx human/mice - how can I use my own annotation and get it into Sleuth?
Thanks in advance
Best wishes, Birgitte