[ensembl-dev] Problems with biomart when trying to use "GRMZM2G" gene IDs for maize

[Dan Bolser]

Hi Carlos,

We recently updated Zea mays to AGPv4 with all new gene annotation from
Gramene.

To browse the old assembly (AGPv3, with GRMZ style notation) you can use:
http://archive.plants.ensembl.org/Maize

We're currently working with Gramene to load the cross references between
the new genes and the old GRMZ genes. In the meantime, GRMZ genes mapped
onto AGPv4 can be viewed in the browser, for example here:
http://plants.ensembl.org/Zea_mays/Share/8580ea57ee94af6de4d0813b580d6e3794453192

Sorry for the inconvenience this change has caused, hopefully the above
information will allow you to continue your analysis.


Many thanks,
Dan.

On Tue, Aug 9, 2016 at 2:16 PM, Vintimilla Carrasco, Carlos <
carlos.vintimillacarrasco at wur.nl> wrote:

> Hello,
>
> I am analysing a Transcryptome Data Set with the Bioconductor package
> BiomaRt. I had no trouble using it during the past month but now it seems
> it does not recognise gene IDs from Maize. Whenever I use the getBM
> function in R it only retrieves values for this gene "zma-MIR319d".  I am
> using listMarts(host="plants.ensembl.org") as host.
>
>
> The same is happening when I try to enter the query list online (
> http://plants.ensembl.org/biomart/martview/45e2918700bd27c5690289d7265b6f
> c5), not of my genes with GRMZM2G notation are recognised.
>
> Am I doing something wrong?
>
> Thank you in advance for your answer.
>
> Carlos?
>
>
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