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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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Feature request: sorted GFF listing paired with selection(s) #1128

Open SamCT opened 5 years ago

SamCT commented 5 years ago

Currently I have a massive GFF file containing a lot of redundant and insignificant protein sequences to my project. It would be extremely efficient if I could view this GFF file as a list, select the gene/protein(s) of interest and have those be highlighted on the track, instead of displaying all that is listed on the track -- I understand I could create a new .bam file but in such a massive list this could be troublesome to parse through.

rbuels commented 5 years ago

that's an interesting idea, what kind of menus or clickable buttons would you envision JBrowse might add to make this possible? Trying to imagine what the UI would look like for this.

nathanhaigh commented 5 years ago

Perhaps the new search dialog in the upcoming release would suit some of your needs @SamCT?

Have a look at the screenshot here: https://github.com/GMOD/jbrowse/pull/1101

cmdcolin commented 5 years ago

This could be a good use of the JBrowse "filter API", sort of an underused but cool feature

https://github.com/cmdcolin/filterplugin

Note that this link to the filterplugin is just a toy example of how filtering API can be used, it's not a plugin built for any purpose.

Making a list of features to choose for filtering on would probably be pretty easy in this sense

nathanhaigh commented 5 years ago

@cmdcolin this has given me some ideas for other things...thanks for pointing this out!