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.
Where is the track metadata?
Track name | Description of data |
Col-CC_Genomic_Annotations_Data | Result of NCBI Eukaryotic Annotation Pipeline |
| Known Reference Sequences | "Alignments of the annotated Known RefSeq transcripts (identified with accessions prefixed with NM_ and NR_) to the genome." (from NCBI documentation) |
| Model Reference Sequences | "Alignments of the annotated Model RefSeq transcripts (identified with accessions prefixed with XM_ and XR_) to the genome." (from NCBI documentation) |
Gnomon Models | One of the inputs into the NCBI Pipeline. "Gnomon annotation of the genomic sequence. Sequence identifiers are provided as accession.version for the genomic sequences and Gnomon identifiers for the Gnomon models:gene.XXX for genes, GNOMON.XXX.m for transcripts and GNOMON.XXX.p for proteins. These identifiers are NOT universally unique. They are unique per annotation release only." (from NCBI documentation) |
| Protein alignment | proteins from other species aligned to v12 protein sequences (verifying this) "Alignments of cDNAs, ESTs and TSAs from other species to the genomic sequence(s). These alignments may have been used as evidence for gene prediction by the annotation pipeline." (from NCBI documentation) |
| TSA alignment | computationally 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 Species | "Alignments of same-species cDNAs, ESTs and TSAs to the genomic sequence(s). These alignments were used as evidence for gene prediction by the annotation pipeline. Sequence identifiers are provided as accession.version." (from NCBI documentation) |
| PFAM domains | Results from an INTERPROSCAN run on the proteins from the V12 prediction to get the PFAM domain information, converted to absolute position on the Col-CC assembly. |
| PFAM domains - Liftoff | Results from an INTERPROSCAN run on the proteins from the Araport11 release to get the PFAM domain information, converted to absolute position on the Col-CC assembly (using the Liftoff file that converted Araport11 coordinates to Col-CC coordinates). |
| PANTHER families | Results from an INTERPROSCAN run on the proteins from the V12 prediction to get the PANTHER family information, converted to absolute position on the Col-CC assembly. |
| PANTHER families - Liftoff | Results from an INTERPROSCAN run on the proteins from the Araport11 release to get the PANTHER family information, converted to absolute position on the Col-CC assembly (using the Liftoff file that converted Araport11 coordinates to Col-CC coordinates). |
| RNA seq tracks | Some tracks are already present. Name is based on the GenBank record, for example, SRR1019221. You can link to that record using this base URL for more information on the experiment: https://www.ncbi.nlm.nih.gov/sra/SRR1019221 (more coming) |
| Long Read alignments | The single Long Read Alignments track is a combination the reads from many individual SRA entries (unlike the RNA seq tracks above). Right clicking on the read itself will allow you to ‘View Details’ and see the ID of the SRA entry for the experiment. Using the id (e.g., SRR11031292), you can go to the full GenBank record for the experiment. https://www.ncbi.nlm.nih.gov/sra/?term=SRR11031292. |
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 an evidence track to the user-created annotation track but I can't!
Right click on the element and select 'Create new annotation' from the menu. Pick the type of element you want to create and it will appear in the yellow track.
The comment or status I typed in hasn't saved. How do I make sure it saves?
For saving comments and gene status, make sure you click outside of the panel where you created the comment to ‘make it stick’.
