Hello !

I don't know what the difference between " ENSG00000002586.1" and "ENSG00000002586.19_PAR_Y" in  Ensembl gene/transcripts ID means.

How do you deal with these ID with "_PAR_Y"  in RNA-seq mapping process ?

Thanks,
Just found out that these suffixes are added in the GENCODE annotation files. We need to discuss how we deal with these because we can't be putting out IDs with one hand and not providing tools that can interpret them with the other hand.

I'm sorry for any confusion.