How To Get All Ensembl Repeatfeatures From Biomart Or The Ensembl Rest Api?

Question

[William]

How can I get all the all the Ensembl RepeatFeatures for a single species from Biomart or the Ensembl REST API?

I don't think the repeats are accessible from biomart (or I cant find them) and I am not sure how to use the Esembl rest API to download all the RepeatFeatures. It would be nice to have the output in the Bed format or something close to it.

Answer 1

[Emily]

Hi William

I'm afraid that's not possible using BioMart or the REST API. BioMart doesn't have access to genomic features such as repeats. The REST API is still in its early stages and has a limited number of endpoints; repeats is not one of them.

The way to get this data is using the Perl API. You can use the RepeatFeatureAdaptor to get all the repeats, then use the RepeatFeature module to print the data you need. It will be easy to print this in Bed format using Perl.

Let me know if you need any help with scripting.

Emily

Answer 2

[Giulietta - Ensembl Helpdesk]

Just to add to this, it is possible through the Ensembl REST, but you have to specify a region:

http://beta.rest.ensembl.org/feature/region/human/3:1000-200000.gff3?feature=repeat

Cheers,
Giulietta

[Andy Yates]

Also you can switch the output to JSON using the following URL http://beta.rest.ensembl.org/feature/region/human/3:1000-200000.json?feature=repeat