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.
What is the meaning of the lower case letters in the nucleotide sequence?
These indicate regions of low complexity. They have not 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 alignment | proteins from other species aligned to v12 protein sequences |
| TSA alignment | computationall assembled transcripts from isoseq experiments aligned to v12 transcript sequences |
(AT-Col-CC-Liftoff-from-TAIR10.1) | (coming: v11 models mapped to v12 reference using Liftoff) |
| (RNA seq tracks) | (coming) |
| (long read seq tracks) | (coming) |
What does the warning symbol mean?
This means that the location and sequence of the splice site needs to be investigated and verified.
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.
- Hack to drag from an undraggable Track:
- Right click on track name in viewer.
- Select 'edit config'.
- Replace the type with : "type": "WebApollo/View/Track/DraggableNeatHTMLFeatures",
- Select 'Apply'
- click and drag the desired feature into the user-created annotations track.