Re: [SO-devel] GFF3 Specification

[Anja T. <an...@eb...>]

On 26 Feb 2013, at 22:50, Joachim Baran wrote:

> Hello,
> 
> On 2013-02-26, at 5:24 PM, Anja Thormann <an...@eb...> wrote:
>> It is not intended to split a chromosome further and if there is a GVF file where this is the case please let me know.
>  I noticed it for this file: ftp://ftp.ensembl.org/pub/release-70/variation/gvf/homo_sapiens/Homo_sapiens_somatic.gvf.gz
> 
>  It contains the following duplication of the Y chromosome:
> 
> ##sequence-region Y 1 10000
> ##sequence-region Y 2649521 59034049

Thank you for spotting this. It is caused by pseudoautosomal regions on the X and Y chromosome (http://www.ensembl.org/info/docs/genebuild/assembly.html).
I will summarise the regions for the next release.

Thanks,
Anja


> 
>> 2) I will revise data where we have "Variant_seq=INSERTION" or "Variant_seq=(11 BP INSERTION)" for the next release.
>> The specification is clear in how the the Variant_seq attribute should be formatted.
>  Thank you.
> 
> Best,
> Joachim
> 
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> SOng-devel mailing list
> SOn...@li...
> https://lists.sourceforge.net/lists/listinfo/song-devel