GRCh38 Annotation for non coding RNA (e.g. miRNA)
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7.8 years ago
Aurelie MLB ▴ 360

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

genome R • 2.6k views
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7.8 years ago
Bert Overduin ★ 3.7k

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

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Hello, Thanks a lot for this comment !

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

Thank you

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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.

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3.8 years ago
wmoss • 0

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

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3.8 years ago
JJ ▴ 600

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

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