[ensembl-dev] GRCh37 Fix Patches - Is Base Numbering Affected?

Bio X2Y bio.x2y at gmail.com
Tue Oct 26 15:45:56 BST 2010

Hi Bronwen,

Thanks for this, I had incorrectly assumed that the fix had been
incorporated into the main chromosome 9. I see that's not the intention.

When I look at HG79_PATCH in the browser, in the updated region, I see a
number of genes with names like 'ASMPATCH00000000003'.

I can't find these genes in the downloadable cDNA or GTF files - is this
because they are considered provisional in some sense?


On Tue, Oct 26, 2010 at 2:58 PM, Bronwen Aken <ba1 at sanger.ac.uk> wrote:

> Hello,
> The base numbering of features (eg. gene annotations) downstream of any
> haplotype, 'fix' patch and 'novel' patch will be calculated on-the-fly by
> our API. The chromosomal positions will be adjusted to take into account any
> difference in length between the haplotype/patch region and the reference
> region that it is replacing.
> When you view HG79_PATCH and then navigate downstream of the patch region,
> you'll see that the gene positions appear different than they would if you
> were looking at the reference chromosome.
> Cheers,
> Bronwen
> On 26 Oct 2010, at 14:43, Bio X2Y wrote:
> > Hi,
> >
> > I was wondering how Ensembl implements the GRCh37 'fix' patches - in
> particular how the numbering of the fixed chromosome is affected.
> >
> > e59 uses GRCh37.p1, which has only one fix patch (HG79_PATCH on chr9).
> Since the new region is larger than the chr9 region it replaces, does this
> mean that the numbering system for the remaining part of chr9 has been
> incremented and  the gene annotations updated accordingly?
> >
> > If not, how are the bases in the new region numbered for the purposes of
> annotation?
> >
> > Thanks
> > _______________________________________________
> > Dev mailing list
> > Dev at ensembl.org
> > http://lists.ensembl.org/mailman/listinfo/dev
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