Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD

Similar Threads
Thread Thread Starter Forum Replies Last Post
Viewing Tophat results in IGV SEQquestions Bioinformatics 19 10-17-2014 12:12 PM
GFF3 display in IGV Alexander Tchourbanov Bioinformatics 2 02-13-2012 12:31 AM
Viewing multiple VCF files in Artemis coldturkey Bioinformatics 0 02-01-2012 02:45 AM
Dindel SAM/BAM format - viewing with IGV EHC General 0 10-06-2011 11:27 AM
From GFF2 to GFF3 tianping Bioinformatics 1 04-18-2011 03:00 AM

Thread Tools
Old 02-03-2010, 01:58 AM   #1
Junior Member
Location: UK

Join Date: Oct 2009
Posts: 6
Arrow Viewing GFF2/GFF3 files on IGV

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.
pratibhamani is offline   Reply With Quote
Old 02-04-2010, 08:54 AM   #2
Location: Nijmegen, Netherlands

Join Date: Jun 2009
Posts: 22

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:

The results are quite nice actually!
Tuxido is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:43 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO