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Old 02-13-2009, 06:42 AM   #1
alperyilmaz
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Default view .wig files

I was trying to view the resulting .wig files generated by FindPeaks3 in IGB (Genoviz at SourceForge) but there's a problem with IGB and cannot parse .wig file correctly. Is there any other alternative software to view .wig files, preferentially along with multiple wig files and a genome.
I tried Argo and IGV, they can parse .wig okay but they didn't allow uploadig a gff file to overlay my own genome with .wig file.
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Old 02-13-2009, 08:48 AM   #2
apfejes
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Well, you could always send the error to me, and I could help you navigate through it, or solve it.. that is also an option. (=

Anthony
(author of FindPeaks)
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Old 02-14-2009, 02:31 AM   #3
alperyilmaz
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Hi Anthony,

thanks for offering help. one of the IGB developers agreed to fix the issue. So it will be fixed soon.
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Old 02-14-2009, 07:58 AM   #4
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Great! Thanks for letting me know.
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Old 02-16-2009, 06:56 AM   #5
lparsons
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I too ran into an issue with FindPeaks and IGB. Basically, IGB complains that there is no track information for each fixedstep start location in the WIG file. From my review of the WIG file specification (http://genome.ucsc.edu/goldenPath/help/wiggle.html) it's pretty ambiguous, but UCSC and other browsers don't complain and it's certainly not necessary information, so a fix in IGB would be best. Please let me know when you hear back from the IGB developers as I would be very interested in the fix. Thanks.
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Old 02-16-2009, 07:59 AM   #6
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Hi Guys,

I haven't used IGB, myself, so I wasn't aware of this problem. Would either of you be able to send an extract from a wig file that does work for their browser? I can certainly modify the headers to match an existing template if you are aware of one that works.

Anthony
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Old 02-16-2009, 08:07 AM   #7
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I don't have a ton of experience with WIG files, but before FindPeaks I hadn't seen one that inserted new "start positions" within a chromosome track before. In other words, added lines like:

fixedStep chrom=chrN start=chromStart step=stepInterval [span=windowSize]

That's probably because I had been used to variableStep format, so for that, I'd just put the new start in the data line.

Using fixedStep like you do is actually more concise, and thus preferable, but I think that is what is causing the problem with IGB. I haven't done too much testing though, so there could be other issues I'm not aware of.

Hope that helps to clear up the situation...
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Old 02-16-2009, 08:13 AM   #8
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That makes sense, although it's difficult to test out without a lot of rewriting. I also have a hard time imagining that there's a browser out there that doesn't understand the fixedStep format of the wig files. Am I really the only one using that format?

At some point, I suppose I could download the IGB source code and look into it, but it's somewhat low on my priority list. If anyone can shed any more light on the subject, or provide a working example of a fixedStep wig that does work with IGB, I'd be happy to spend some time on it.
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