Disappearing ref genome and data track

[Harry Akligoh]

After loading my gene list which is compatible with my reference, reference genome disappears and the gene list doesn't show. How can i fix this issue.

[igv-help]

Looking into this, I see that IGV does not handle it well if NONE of the loci/genes in the gene list are found in the reference genome. It will produce the empty screen you see and you may have to restart IGV. However, you should have seen an error message pop up before things went blank. 

I see that you have a custom genome loaded. In that case, IGV will not recognize any gene names. Try using the genomic coordinates instead.

[igv-help]

Hi again,

It just occurred to us that perhaps you are trying to load gene annotations via the gene list dialog. That is not what gene lists are for.They are used to specify genomic regions to view in a multi-locus view, ie where you view multiple regions side by side in the IGV window.  If our documentation about the gene list dialog was confusing, we will fix that. To load a genome annotation track, you load an annotation file via the  File menu.