Hello, After executing featureCounts on my BAM file using a built-in genome (hg38) from Galaxy I have obtained the table with the Geneids and the number of reads mapped to them. I am trying to find where is the built in annotation file in Galaxy in order to know to which gene/feature each of the Geneids (numbers) reffer to. But I don't manage to find it. Does someone know where can I find the annotation file? Thank you, Mercedes
The built-in annotation files used by featureCounts can be found within the Subread package here: https://sourceforge.net/projects/subread/files/
But those files have no gene names, just the Entrez gene identifiers (e.g. 497097). If you want gene names you can get those for the Entrez identifiers with the annotateMyIDs tool in e.g. this Galaxy https://usegalaxy.eu/.
Hope that helps!
P.S. I've added some info on the annotation to the featureCounts wrapper now.