[BioC] mm10 goseq supported genome

[Nadia Davidson]

Vincenzo Capece <vivo0304 at ...> writes:

> 
> Dear all,
> I am trying to analyze RNA seq data with goseq but I have a problem:
> mm10(the reference genome that I am using for my experiment) is not
> supported by goseq. The last version supported by goseq is mm9.
> Can you help me to annotate mm10 RNA seq data with goseq?
> The version of my goseq is: 1.8.0.
> Thanks in advance.
> Regards,
> 
>          Vincenzo
> 
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Hi Vincenzo,

Indeed it looks like genLenDataBase has not been updated to support 
mm10, so I will try to rectify this.

In the mean time, I have updated goseq so that it attempts to 
download the gene length information from UCSC if it's missing 
from genLenDataBase. This is a bit slower, but should work just as well. 
The fix will be in goseq version 1.11.2 onwards. Email me if you want the 
source code sooner than it becomes available on 
http://bioconductor.org/packages/2.12/bioc/html/goseq.html. 
Which annotation are you using by the way?

Cheers,
Nadia.