Viewing GFF2/GFF3 files on IGV

[pratibhamani]

Hello evryone,


I am trying to visualize GFF2/GFF3 files on IGV. But even after uploading the file, nothing seems to be visible on the screen? IGV does support it.

Has anyone faced this problem or is there any other setting which i am supposed to do?

Kindly help asap.

[Tuxido]

You should use the sam files to view the sequence alignments in IGV. The gff3 does not work and will also not be supported in the future by lifetech.
You need to do a few conversion to the sam files before you can use them in IGV. You need to convert them to .bam files and generate corresponding index files.
This webpage show you how to do that: http://seqanswers.com/forums/showthread.php?t=2441

The results are quite nice actually!