Question: JBrowse help with opening a Gff gene model file
0
gravatar for Hwaterma
12 months ago by
Hwaterma0
Hwaterma0 wrote:

I am trying to look at my gene model on JBrowse and keep getting "an error was encountered when displaying this track. Diagnostic message: [object ProgressEvent]". I can't seem to find what it mean anywhere. Can someone please help?

jbrowse • 349 views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 12 months ago by Hwaterma0
1

Can you try converting the GFF3 into a json track and see what would happen? That may give you more information if anything goes wrong. Also, it is usually useful to run a GFF3 check using gff_validator, even though your GFF3 seems to be fine.

http://genometools.org/cgi-bin/gff3validator.cgi

ADD REPLYlink written 11 months ago by Vitis2.3k

I am presuming you mean convert to json using bin/flatfile-to-json.pl --gff yourfile.gff --trackLabel. Just wanted to clarify that in case it was unclear for Hwaterma

ADD REPLYlink written 11 months ago by cmdcolin1.3k
1

Thanks for clarifying that for me!

ADD REPLYlink written 11 months ago by Vitis2.3k

Hi Hwaterma, I'm a JBrowse dev. It is hard to debug this without more info. If you can share any more data or info about your setup let me know

ADD REPLYlink written 12 months ago by cmdcolin1.3k

Here is the top of my GFF file:

##gff-version 3
utg002023l_pilon    .   contig  1   648515  .   .   .   ID=utg002023l_pilon;Name=utg002023l_pilon
utg002023l_pilon    maker   gene    52467   53191   .   +   .   ID=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1;Name=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1
utg002023l_pilon    maker   mRNA    52467   53191   405 +   .   ID=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1;Parent=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1;Name=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1;_AED=0.24;_eAED=0.27;_QI=0|1|0|1|0|0|2|0|134
utg002023l_pilon    maker   exon    52467   52596   .   +   .   ID=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1:exon:36371;Parent=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1
utg002023l_pilon    maker   exon    52917   53191   .   +   .   ID=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1:exon:36372;Parent=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1
ADD REPLYlink modified 11 months ago by ATpoint35k • written 12 months ago by Hwaterma0

How is this track opened? Did you use the Track->Open track inside JBrowse or loaded via command line? Also the formatting on this gff is messed up by posting so it's hard to tell if it's formatted right, but a cursory look appears to not have anything wrong

ADD REPLYlink written 12 months ago by cmdcolin1.3k

I am on the online JBrowse and I click on Track. That opens a pull down menu. Then I click on open track file or URL. The it make a track for me but says the error instead of my info.

ADD REPLYlink modified 11 months ago • written 11 months ago by Hwaterma0

What browser are you using? I do not get any error doing this in a local instance

ADD REPLYlink written 11 months ago by cmdcolin1.3k
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