Problems with display in IGV

keo · 01-31-2012, 04:23 PM

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 · 02-01-2012, 06:04 AM

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 voilà, it works fine.
Keo.

Jim Robinson · 02-02-2012, 06:55 AM

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

keo · 02-02-2012, 07:23 AM

Thanks Jim,
I'll keep this in mind.
Best,
Keo.

Jim Robinson · 02-02-2012, 07:27 AM

Sure, to emphasize this only works for indexed fastas. You can index them with samtools.

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01-31-2012, 04:23 PM	#1
keo Junior Member Location: Mexico City Join Date: Jan 2012 Posts: 8	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.

02-01-2012, 06:04 AM	#2
keo Junior Member Location: Mexico City Join Date: Jan 2012 Posts: 8	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 voilà, it works fine. Keo.

02-02-2012, 06:55 AM	#3
Jim Robinson Member Location: Boston, MA Join Date: May 2009 Posts: 75	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

02-02-2012, 07:23 AM	#4
keo Junior Member Location: Mexico City Join Date: Jan 2012 Posts: 8	Thanks Jim, I'll keep this in mind. Best, Keo.

02-02-2012, 07:27 AM	#5
Jim Robinson Member Location: Boston, MA Join Date: May 2009 Posts: 75	Sure, to emphasize this only works for indexed fastas. You can index them with samtools.