displaying RepeatMasker .gff3 in IGV

[joa...@gmx.com]

Hi, I have RepeatMasker output for one contig of a reference genome, and have converted the RM*.out to RM*.gff3, as described here:

https://www.biostars.org/p/19190/

When I load this file into IGV, I get only an empty track. Is there a step I have missed to align it to the reference perhaps?

Thanks for any suggestions!

[joa...@gmx.com]

Got it! My contig was named differently when I masked it. Working fine now :)

[Jim Robinson]

Good, and that's a useful link I wasn't aware of it.