[ensembl-dev] Ensembl with Human Patches Question

Susan Fairley sf7 at sanger.ac.uk
Wed Apr 4 14:42:17 BST 2012

Hi Will,

We align human ESTs to the primary chromosomes as part of the build for 
the primary assembly.

For the patches, we use a different 'lightweight' process, which does 
not include aligning ESTs. Consequently, we have no EST alignments to 
the patches and don't display them on the website.

I hope that helps to explain things. Please let me know if you have any 
further questions.

Kind regards,

Will Chow wrote:
> Hi,
> I'm not sure if this is a core code or a webcode thing, or perhaps I'm 
> using this wrong, hence why I'm submitting this here and not one of the 
> rt queues.
> This was found via the ensembl browser specifically involving the human 
> patches.  For example the first patch on chr 1.
> Turning on the Human EST and marker Track:
> http://www.ensembl.org/Homo_sapiens/Location/View?db=core;r=1:31872759-32017063 
> The track reveals the features under the clone AC114494. 
> <http://www.ebi.ac.uk/ena/data/view/AC114494>
> If I were to jump to the patched region via the assembly exceptions track.
> http://www.ensembl.org/Homo_sapiens/Location/View?db=core;r=HG989_PATCH:31872759-32024309 
> Under the same clone, AC114494, these features don't appear.
> I would've thought the features would appear here as well.  Can someone 
> shed some light on this?
> thanks
> Will
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