Annotation for miRNA-seq data analysis

Question

[Arindam Ghosh]

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.

Answer 1

[Astrid_Ensembl]

Ensembl imports miRNAs from miRBase: https://www.ensembl.org/info/genome/genebuild/ncrna.html

[Arindam Ghosh]

Exactly! This is why I was curious to know why most studies separately use miRBase annotations for miRNA even though they are already in the Ensembl reference genome. So I believe there should not be any harm in using the Ensembl GTF file with featureCounts for estimating miRNA expression.