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c. positions

asked 2016-05-16 11:35:25 -0600

Kyle Williams gravatar image

Hello,

Is there any way that one could view the c. position for a specific transcript while looking in genome browse? A good example of what I would be looking for would be a set up like Alamut's.

Thank you for your time,

Kyle

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answered 2016-05-17 16:40:38 -0600

Hi Kyle,

Visualizations in GenomeBrowse are limited to what is available within the annotation sources or data files that are currently loaded into the window, we do not perform any type of computations on the data. With variant sources there are a few annotation sources that will provide c. notation for the variant.

The most comprehensive source is the ExAC VEP Annotations 0.3, BROAD source that is available from the Public Annotations repository (File > Add). If you load this source any variant in your data that is also in the ExAC track will contain this information.

image description

To make the HGVS c. notation the label on the plot just hover your mouse over the ExAC plot and you should see a gear icon appear in the upper left corner, just click the icon to change the labels.

Let me know if you have further questions.

Thanks, Jami...

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Asked: 2016-05-16 11:35:25 -0600

Seen: 17 times

Last updated: May 17 '16