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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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Add sequence search track: too long names #1417

Closed billzt closed 3 years ago

billzt commented 5 years ago

File -> Add sequence search track, input a sequences of about 20-30 bases

The label is solong that it covers the shown track!: 1

What should be better is: 2

I think this could be done (input a short name) in the pop dijitDialog in future.

colindaven commented 5 years ago

+1 True, had same usability issue here

cmdcolin commented 5 years ago

I know this doesn't really answer the question but if you are doing serious sequence searches with JBrowse, I would recommend setting up a BLAT/BLAST backend e.g. with sequenceserver. I think the RegexSequenceSearch doesn't necessarily scale too well and has some known issues with longer sequences #833

cmdcolin commented 5 years ago

I guess if it is desirable we can try and find fixes for things like #833 but that's just my perspective on sequence searching

billzt commented 5 years ago

@cmdcolin Thanks for your suggestion. How to setup a BLAT/BLAST backend within JBrowse? Would it be difficult?

cmdcolin commented 5 years ago

There is not necessarily a prescribed way to do this

It would be nice to have "recipes" for example, but I have only done it with sequenceserver https://jbrowse.org/docs/faq.html#how-can-i-link-blast-results-to-jbrowse

billzt commented 5 years ago

Well, in fact I mainly use this "search" function to locate primer/oligo sequences in 10~30nt, which seem not suitable to be searched in BLAST.

cmdcolin commented 4 years ago

Maybe BLAT then, which would need a custom backend

ValWood commented 4 years ago

The label obscuring the data is an issue with many track types. https://github.com/pombase/website/issues/1596 Scrolling left and right the required amount to see the features and labels clearly is too tricky...

It would be nice if there was a bit of headroom between the label and the data track.

cmdcolin commented 4 years ago

One option that globally affects all tracks is setting

https://jbrowse.org/docs/global_options.html

trackLabels=no-block

In the jbrowse.conf. It is a valid concern. Might be interesting if the user can toggle this setting per track, or toggle the setting without having the admin reconfigure it

cmdcolin commented 3 years ago

Add the option to create your own track label to the dev branch of this repo

cmdcolin commented 3 years ago

feature added in 1.16.11