<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>Yes, the ASMPATCH genes are provisional in that they are annotated by a basic pipeline instead of the full genebuild pipeline. This is why we do not give them a standard Ensembl stable ID like ENSG00000000003</div><div><br></div><div>The genes on 'patch regions' are stored in the 'otherfeatures' database and not in the 'core' database where the official gene set can be found. This means that they will not be dumped out to the FTP site.</div><div><br></div><div>Cheers,</div><div>Bronwen</div><div><br></div><div><br><div><div>On 26 Oct 2010, at 15:45, Bio X2Y wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Bronwen,<div><br></div><div>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.</div><div><br></div><div>When I look at HG79_PATCH in the browser, in the updated region, I see a number of genes with names like 'ASMPATCH00000000003'.</div>
<div><br></div><div>I can't find these genes in the downloadable cDNA or GTF files - is this because they are considered provisional in some sense?</div><div><br></div><div>Thanks.</div><div><br></div><div><br><div class="gmail_quote">
On Tue, Oct 26, 2010 at 2:58 PM, Bronwen Aken <span dir="ltr"><<a href="mailto:ba1@sanger.ac.uk">ba1@sanger.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hello,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Cheers,<br>
Bronwen<br>
<div><div></div><div class="h5"><br>
On 26 Oct 2010, at 14:43, Bio X2Y wrote:<br>
<br>
> Hi,<br>
><br>
> I was wondering how Ensembl implements the GRCh37 'fix' patches - in particular how the numbering of the fixed chromosome is affected.<br>
><br>
> 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?<br>
><br>
> If not, how are the bases in the new region numbered for the purposes of annotation?<br>
><br>
> Thanks<br>
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