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My Apollo window has frozen. What do I do?

Try reloading your browser window.

  • For Chrome: Shift Command R
  • For Firefox: Ctrl+R
  • For Safari: shift+reload

Some data tracks are very slow to load. 

The way JBrowse works within Apollo, the first time your load up a track it might take a while. But once loaded, any successive loads will be quicker.

I used to see tracks and now they are gone.

Close the track and open it again. Yes, this is the standard 'turn it off and turn it on again' solution.

What is the meaning of the lower case letters in the nucleotide sequence?

These indicate regions of low complexity. They have no impact/implication with respect to annotation.

Is it possible to know which organism is the source for a particular protein alignment (in the Protein Alignment track)?

By right clicking on the alignment, and then selecting 'View details.' You'll see the GenBank accession in the id section and can search for that at NCBI.

Tell me more about the tracks I see.

Track name

Description of data

Col-CC_Genomic_Annotations_Data

Result of NCBI Eukaryotic Annotation Pipeline

Gnomon Models

one of the inputs into the NCBI Pipeline

Protein alignmentproteins from other species aligned to v12 protein sequences
TSA alignmentcomputationally assembled transcripts from isoseq experiments aligned to v12 transcript sequences

AT-Col-CC-Liftoff-from-TAIR10.1

v11 models mapped to v12 reference using Liftoff

Col-CC Same Speciesproteins from Arabidopsis aligned to v12 protein sequences
(RNA seq tracks)

(coming)

(long read seq tracks)(coming)

What does the warning symbol mean?

This symbol means that the location and sequence of the splice site needs to be investigated and verified because it does not conform to the GT-AG rule.

How do I see genes that need secondary review?

In the Annotations tab of your right hand panel, click on the dropdown for "All Statuses" and select the status you want to filter the annotations to review.

I want to drag an element from a track but I can't!

Here's a hack to drag from an undraggable Track by updating the track configurations only for your view. Settings will reset when you reload/exit the browser/logout.

  • Right click on track name in viewer.
  • Select 'Edit config'.
  • Replace the WebApollo/View/Track type configuration with : "type": "WebApollo/View/Track/DraggableNeatHTMLFeatures",
  • Select 'Apply'
  • Click and drag the desired feature into the user-created annotations track.
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