For RNA-seq (mRNA/lncRNA) data analysis, we can use reference genome and annotation from Ensembl (GRCh38). Can the same annotation file be used for miRNA-seq data analysis? Even though miRNA annotations are present in Ensembl, most works that I have come across use annotations from other databases like miRBase. Is there any specific reason for this that I am missing out? Ensembl genomes/annotations are convenient to use as they contain all gene biotypes in a single place.