Trouble adding Annotations

[Christopher Corcoran]

I've been able to upload my genome for Pseudomonas aeruginosa PAO1, and I am able to visualize my RNA Seq BAM files against the genome. However I am having trouble visualizing the gene annotations. I have attempted to load in .gff3 and .gtf files for the gene annotations. While a track appears in the window, there are no annotations shown, just a blank track. How can I get these to display? I have been downloading sequences and annotations from pseudomonas.com (https://pseudomonas.com/strain/show/107) as well as from UCSC Genome archive. Thank you in advance!

[igv-help]

A screenshot would be helpful. 

And also a copy of the IGV log from your session when you try to load the annotation file. The log file is in the igv folder in your user home. It will be named something like igv0.log.

[Christopher Corcoran]

Sorry, thought I attached the screenshots before. Here is the screenshot as well as the log after attempting to upload the annotations.

[igv-help]

This can be caused by 2 things.  (1) there are no annotations at the location you are viewing,  or (2) the sequence (chromosome) names in your GFF or other annotation file differ from the names in the fasta you loaded to define the reference.  Given a fasta chromosome name like "refseq|NC_002516.2_chromsome..."  I think the second cause is likely.

Soon we will allow loading of complete genomes including their annotations for the UCSC GenArks repository. https://hgdownload.soe.ucsc.edu/hubs/.    That will make loading much easier.  That should be available last October or early November.   In the meantime you either need to fix the names in your fasta file or your GFF file so that they match.

[James Robinson]

A couple of other options in dealing with the chromosome names.   You do not really have to change them in the fasta, you can change them in the index (the .fai file).   It is a plain text file.   Secondly, if you are using a genome "json" file you can add a pointer to an aliasURL as described here:  https://github.com/igvteam/igv.js/wiki/Reference-Genome