Question: GRCh38 Annotation for non coding RNA (e.g. miRNA)
0
gravatar for Aurelie MLB
3.7 years ago by
Aurelie MLB290
United Kingdom
Aurelie MLB290 wrote:

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

R genome • 1.1k views
ADD COMMENTlink modified 3.7 years ago by Bert Overduin3.6k • written 3.7 years ago by Aurelie MLB290
1
gravatar for Bert Overduin
3.7 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

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

ADD COMMENTlink written 3.7 years ago by Bert Overduin3.6k

Hello, Thanks a lot for this comment !

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

Thank you

ADD REPLYlink written 3.7 years ago by Aurelie MLB290

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.

ADD REPLYlink written 3.7 years ago by Bert Overduin3.6k
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