Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference?
UCSC chromosome names begin with the prefix
chr, but Ensembl chromosome names do not. For example, chromosome 19 would be denoted as
chr19 in UCSC, and as
19 in Ensemble. Most tools would view those as different when looking for matches/overlaps. Therefore it is always a good idea to make sure these match before you perform any downstream analysis.