Should ENSG IDs be annotated with the same patch as for the counts or with the latest release?

Question

[lm687]

Say I have counted the reads in a bam file using GRCh38.82 - a reasonably recent patch but not the latest. When I annotate genes, is it best to tell biomart to use as host the GRCh38.82 annotation or to use GRCh38.88 (which is currently used by default, as far as I'm concerned), in which case the ENSG IDs which have been deprecated since will be converted into an NA and can be removed? (Of course, the optimal solution would be to do everything with GRCh38.88...) Thank you

Answer 1

[BioinfGuru]

It won't make much of a difference either way.... I wouldn't worry about it. Go with the latest if it is no trouble.