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flekschas / enhancer-gene-vis

A tool for visualizing ABC enhancer-gene connections in the context of genetic variants.
https://flekschas.github.io/enhancer-gene-vis
Apache License 2.0
12 stars 4 forks source link

enhancement: support other classes of structural variations #4

Open zhilongjia opened 3 years ago

zhilongjia commented 3 years ago

It will be great if it can show a custom track, like the UCSC genome browser.

Updated: My goal is to check whether SV break an enhancer or not. Currently, it is not easy to get the location of a certain SV (using a mouse pointer). Thank you.

although it has a custom default track already, another track to show where is the SV segment among this default track will show genes nearby, which is important to the SV.

As an SV may disrupt an enhancer, so it will great to make an (column of) enhancer-centred view, besides the gene-centred view.

flekschas commented 3 years ago

It will be great if it can show a custom track, like the UCSC genome browser.

I am working on a feature to allow you to customize the entire view but you will have to use the HiGlass/Resgen(https://resgen.io) ecosystem.

Could you specify what kind of track you would like to load? At the moment you can at least already browse a custom bed track. This might already help you correlate SV with enhancers.

Currently, it is not easy to get the location of a certain SV.

Can you clarify? Navigating to a certain location is simple. Or do you mean something else?

zhilongjia commented 3 years ago

I also made some update about my question.

Currently, it is not easy to get the location of a certain SV.

if a SV is within a custom track, it will be difficult to know the exact location of the SV.

If the custom track on the left is used only to show the SV itself, the nearby genes of the SV will be not shown. Thank you.

flekschas commented 3 years ago

I think I get your request. Supporting the structural variations-aware manner would indeed be cool. Unfortunately, I can't give you any time lines as this would be a pretty involved feature.

zhilongjia commented 3 years ago

Showing genomic features, like structural variations, is great. Here a quick way is to use the input of users, not to load structural variations from a public database as the structural variations are relatively sparse in the genome. Thank you.