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

Bronwen Aken ba1 at sanger.ac.uk
Tue Oct 26 14:58:54 BST 2010


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.


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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 2058 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20101026/aebbfbb3/attachment.p7s>

More information about the Dev mailing list