SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
GFF3 display in IGV Alexander Tchourbanov Bioinformatics 2 02-13-2012 12:31 AM
IGV - Genome problems tonio100680 Bioinformatics 7 01-12-2012 09:09 AM
missing reads in IGV display cswarth Bioinformatics 2 06-28-2011 09:30 AM
IGV: display six-frame (amino-acid) translation of reference genome? d f Bioinformatics 2 03-07-2011 03:57 PM
IGV display of coverage john_mu Bioinformatics 2 06-05-2010 11:40 PM

Reply
 
Thread Tools
Old 01-31-2012, 04:23 PM   #1
keo
Junior Member
 
Location: Mexico City

Join Date: Jan 2012
Posts: 8
Default Problems with display in IGV

Hello everybody,
I hope this is not off topic, I'm new in this forum.
I have installed IGV 2.0.34 on two Windows computers, one 32bit Vista
and another Windows7 64bit with graphics accelerator. IGV loads
normally in both machines. I can open and see .bam files with no
problem on the 32bit machine, but when I try to open the exact same
files in the 64bit W7 it appears to open the file, but I can't see the
reads or any other of the tracks. When I pass the mouse over the
screen it gives me the read data, but I can't see the grey bars, nor
the bases. Furthermore, the pop up read information doesn't dissapear.
It would appear it is only a display problem, but I have tried several
approaches but to no avail, including:
- Checking that Java is updated.
- Zooming in and out of the window.
- Selecting large, medium and small genome regions.
- Changing the screen resolution to all possible values.
- Changing the display from 32 to 16 bit color.
- Disabling the graphics accelerator.
Has anyone had this problem? Any ideas on what else to try?
Thank you very much for your help.
Keo.
keo is offline   Reply With Quote
Old 02-01-2012, 06:04 AM   #2
keo
Junior Member
 
Location: Mexico City

Join Date: Jan 2012
Posts: 8
Default

Hi all,
Problem fixed.
The IGV help team mentioned that the problem might be the reference, and I realized that my .genome file was built on the 32bit Vista machine. I just rebuilt the .genome file directly in my 64bit from the fasta of my reference instead of using the one built in the 32bit systems, and voilą, it works fine.
Keo.
keo is offline   Reply With Quote
Old 02-02-2012, 06:55 AM   #3
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Hi Keo,

I've looked at your problem and logs a little more, and for the sake of others who might search this forum let me clarify. I think your problem stemmed from trying to move the .genome file between machines, not a 32 vs 64 bit issue. The .genome file is a zip that contains, among other things, the file path to the sequence folder. If you move it the path might not be valid anymore. This can be fixed by unzipping the .genome file (e.g. using winzip) and editing a property file, then rezipping.

We now support indexed fastas as an alternative to the .genome file & directory. You have to load annotations separately using this option, but it is much cleaner if you anticipate moving the fasta around or sharing it. To load the fasta just use the "load genome" option (no need to import).

Jim
Jim Robinson is offline   Reply With Quote
Old 02-02-2012, 07:23 AM   #4
keo
Junior Member
 
Location: Mexico City

Join Date: Jan 2012
Posts: 8
Default

Thanks Jim,
I'll keep this in mind.
Best,
Keo.
keo is offline   Reply With Quote
Old 02-02-2012, 07:27 AM   #5
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Sure, to emphasize this only works for indexed fastas. You can index them with samtools.
Jim Robinson is offline   Reply With Quote
Reply

Tags
igv

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 12:48 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO