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
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Aurelie MLB
If you have a little patience, Ensembl's release 76, which is based on GRCH38, is imminent: The new human annotation is almost here!
Hello, Thanks a lot for this comment !
How do you usually access this? Is there some convenient tools? Anything in bioconductor (Biomart ?)?
Thank you
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.
The RNACentral database has hg38 annotations for ncRNAs - ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/genome_coordinates/
Gencode is my choice: https://www.gencodegenes.org/releases/current.html
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