myGene in R using different genome assembly

Question

[manu.tiwari]

Hello I am using myGene in R for annotation. The available list of genome assemblies is a bit outdated (dm3 for Drosophila melanogaster). For instance, I would like to use BDGP6 (dm6) for Drosophila melanogaster which is the latest release. Is there a way to do this?

Thanks. M

Answer 1

[Newgene]

Hi @manu.tiwari, MyGene.info API (the web API underlying the mygene R package) is keeping updated from NCBI, Ensembl, UCSC and many other resources. For example, Ensembl data were updated to version 89; UCSC data were updated on 20170608. So the Drosophila melanogaster annotation data from MyGene.info are on dm6 already. The up-to-date metadata info can always be accessed at http://mygene.info/metadata.

But you are right, our documentation is out-dated. Unfortunately, that "Genome assemblies" table still requires manually updated. I have just updated our documentation page:

http://docs.mygene.info/en/latest/doc/data.html#genome-assemblies

(BTW, our latest documentation is now on http://docs.mygene.info, the link you provide is no longer updated. We will try to setup a proper redirection for the old links soon.)

Glad you found MyGene.info useful for your project and thanks for pointing this out!

MyGene.info team

Answer 2

[andrew.j.skelton73]

This won't directly answer the question, but have you considered switching over to biomaRt?? - You'll be able to get up to date annotations that way, as it directly queries Ensembl's databases.

[manu.tiwari]

Thanks for the comment. I am using biomart but was wondering if it would be possible using mygene as well.

[andrew.j.skelton73]

Judging by the vignette, it seems that it can export data, but importing custom datasets isn't available.