genes track missing

[Findley Ransler]

I am teaching a genomics course and we are using IGV 2.3 on Macs (local download to each students computer).  One of my students is having some issues.  The main issue is that she is unable to get the genes track to view.  It worked previously on her computer and it works fine on several other student's computers.  She made a new .genome file, with the same fasta and gff file) and is still having issues.  Her second issue is that the tick-marks in the zoom bar are not loading properly.  When she zooms out, they are not present.  However, the re-appear when she zooms way in.  

She did have to install Java (8) for IGV to work on her computer.  Could the issue be that she is running on Java 8 and not Java 7?  Any other thoughts?

Thanks,

Findley

[James Robinson]

This is not a java issue, from the symptoms I suspect it is an issue with either the gff file or the fasta index file, but I would need to see the files to be sure.     I would suggest she try load the fasta file directly as the reference (Genomes > Load from file > fasta file),  the load the GFF file from the file menu.   This will help pinpoint the problem.   Also,  perhaps delete or rename the fasta index file (.fai file) and let IGV recreate it when the fasta is loaded.   Be patient this can take some time.

You could also try shutting down IGV and deleting or renaming the "igv" folder to do a complete reset,  then restart.

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