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GMOD / JBrowseR

R interface to the JBrowse 2 Linear Genome View.
https://gmod.github.io/JBrowseR/
Apache License 2.0
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Error: HTTP 404 fetching output.gff.tbi #40

Open WSCAAA opened 4 months ago

WSCAAA commented 4 months ago

When I tried to use my local .gff file in shiny, I got this error. And I found that the detail about the output.gff track is

config.type FeatureTrack config.trackId GRCh38_output config.name output config.assemblyNames GRCh38 config.adapter.type Gff3TabixAdapter config.adapter.gffGzLocation output.gff config.adapter.index.location output.gff.tbi But when I tried to upload this .gff file to JBrowseR Desktop I find that when the config.adapter.type is Gff3Adapter, the track can be load. I wonder if there is a way to change config.adapter.type in shiny.

cmdcolin commented 4 months ago

you might want to try to convert to gff tabix, which would have the gff3.gz and the gff3.gz.tbi

we could review plaintext gff support in JBrowseR but tabix is probably best if possible, especially for human genome annotation gff

WSCAAA commented 3 months ago

I'm trying to figure out if I need to have a file that includes both sorted_output.gff.gz and sorted_output.gff.gz.tbi. However, I'm encountering errors that say "Error in check_gff(track_data): feature data must be GFF3. Use .gff or .gff3 extension". Here's the relevant part of my code:

# Create configuration for a JB2 GFF FeatureTrack
annotations_track <- track_feature(
    "output.tabix",
    assembly
)

Can you help me with this issue?


![image](https://github.com/GMOD/JBrowseR/assets/58099667/c8210cb9-1711-4cf2-b806-fbb7999d6488)