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 The available list of genome assemblies is a bit outdated (dm3 for Drosophila melanogaster).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
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manu.tiwari •
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(BTW, our latest documentation is now on http://docs.mygene.info, the link you provide is no longer updated.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
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.
Thanks for the comment. I am using biomart but was wondering if it would be possible using mygene as well.
Judging by the vignette, it seems that it can export data, but importing custom datasets isn't available.
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