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how to view a 600MB wig file
Hi, I'm not bioinformatician, so you may find this question stupid. We sent samples to other institute for chip-seq (solexa system) and they gave us both text file and wig file, which was supposed to be able to be viewed with genome browser at UCSC. But the file is too huge to upload. Is there a software that I can view the huge wig file on my computer? Thanks for your help.
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You may be able to use the "Integrated Genome Browser" IGB to view the WIG file. It is based on the opensource GenoViz SDK. You can find more information here: http://genoviz.sourceforge.net/ -
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You can also break up the Wig files - many people have tools for that handy, or they can be written very easily.
A lot of the time people cram all of the chromosomes into a single wig file, which is then too big to load. (I don't know if that's the case here.) I often find it's easier to view them one chromosome at a time, which gives you MUCH smaller files.The more you know, the more you know you don't know. —AristotleComment
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I think you should be able to upload it if you gzip it first, but best would be to filter it first to remove all positions below a cutoff (it is no point showing positions with only one or two reads). Perhaps the easiest would be to run the eland files through FindPeaks to get a filtered wig file...
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Thanks - I always assume wig files are gzipped and filtered, but I guess that's not always the case! Just a by-product of working with FindPeaks all the time. (-; Both of those are good ideas too.
AnthonyThe more you know, the more you know you don't know. —AristotleComment
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Thank you all very much!Comment
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Wig2Bar app
I've written an application called Wig2Bar which will convert your wig file into binary, chromosome specific, bar files that can be directly uploaded into the Integrated Genome Browser.
See http://useq.sourceforge.net/cmdLnMenus.html#Wig2Bar and http://useq.sourceforge.net/ for download, installation, and usage instructions.
I use this to convert UCSC tracks. -cheers, DavidComment
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