How to customize the looks of dynamically generated tracks in jbrowse?
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3.8 years ago

Hi!

I have some trouble visualizing data in jbrowse.

I have a whole lot of gff3 file like this:

##gff-version 3

chr1          test      tfbs    101375  101425  .       +       .       ID=test001;Name=test-motif

chr1          test      summit  101400  101400  .       .       .       Parent=test001;Name=test-summit

And I add them to my jbrowse like so:

http://the.url.of.my.web.page/path/to/jbrowse/index.html?tracks=DNA,ucsc-known-genes,test&addStores={"test" : {"type" :"JBrowse/Store/SeqFeature/GFF3","baseUrl" :".","urlTemplate" :"data/tmp.gff3" }}&addTracks=[{"label" :"test","type" :"JBrowse/View/Track/CanvasFeatures","store" :"test" }]&loc=chr1:100879..101838

It actually works fine, however the summit is impossible to see.

If I alter the gff3 to look like the following, It has a perfect look but now is labelled "mRNA" and "CDS":

##gff-version 3

chr1         mRNA      tfbs    101375  101425  .       +       .       ID=test001;Name=test-motif

chr1          CDS      summit  101400  101400  .       .       .       Parent=test001;Name=test-summit

My question is how to change the drawing behaviour of jbrowse to draw "tfbs" like "mRNA"?

----#----> instead of ########>

Any help would be appreciated! Thanks!

Levi

ChIP-Seq jbrowse • 1.0k views
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Entering edit mode
3.8 years ago
cmdcolin ★ 2.1k

When I use the same config that you have initially e.g.

cat test.gff
chr1    test    tfbs    101375  101425  .       +       .       ID=test001;Name=test-motif
chr1    test    summit  101400  101400  .       .       .       Parent=test001;Name=test-summit

With this URL

http://localhost/jbrowse/index.html?tracks=test&addStores={"test" : {"type" :"JBrowse/Store/SeqFeature/GFF3","baseUrl" :".","urlTemplate" :"test.gff" }}&addTracks=[{"label" :"test","type" :"JBrowse/View/Track/CanvasFeatures","store" :"test" }]&loc=chr1:101366..101452&highlight=

I get the ------#------> output as you expected I think....

enter image description here

I know there are some cases where you get a solid box where you want subfeatures but I appear to get the subfeature in this case

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Ok, this is strange. I just copied what you wrote and got this:

http://summit.med.unideb.hu/jbrowse/Screenshot_2018-07-30_JBrowse_chr1_101362_101457.png

Could you please say, what version of jbrowse are you using?

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I'm using the latest 1.15 version. I tested the 1.12.5 release and can indeed see that this version does not plot subfeatures like your screenshot has. I can't recall exactly what would be the thing that changed that fixed this per se but if you can upgrade you might consider that!

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Entering edit mode

Hi Colin,

Thanks! I upgraded Jbrowse and now it works.

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