GRCh38 Annotation for non coding RNA (e.g. miRNA)

Question

[Aurelie MLB]

Hello,

Would someone know what tool to use to annotate positions in the Homo Sapiens GRCh38 genome with non coding RNA ids ? I would like to find the miRNA for instance.

I am using Bioconductor right now. Is there any library I could use?

Many thanks

Answer 1

[Bert Overduin]

If you have a little patience, Ensembl's release 76, which is based on GRCH38, is imminent: The new human annotation is almost here!

[Aurelie MLB]

Hello, Thanks a lot for this comment !

How do you usually access this? Is there some convenient tools? Anything in bioconductor (Biomart ?)?

Thank you

[Bert Overduin]

You can indeed use the web interface to BioMart or the Bioconductor biomaRt package. But you also can access Ensembl using a Perl API, by direct MySQL queries and through a REST API. And there is an ftp site as well. It depends all a bit on what you exactly want to do, what is the best option for you. More info you can find in the Ensembl documentation.

Answer 2

[wmoss]

The RNACentral database has hg38 annotations for ncRNAs - ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/genome_coordinates/

Answer 3

[JJ]

Gencode is my choice: https://www.gencodegenes.org/releases/current.html