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
•
written
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kontra.levente
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....
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
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?
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!
Hi Colin,
Thanks! I upgraded Jbrowse and now it works.
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