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Old 12-16-2010, 04:22 AM   #1
khb
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Question convert wig to bigwig

I've used MACS and got one wig file per chromosome. I want to make a bigwig file and used the manual on ucsc http://genome.ucsc.edu/goldenPath/help/bigWig.html.
1. Should I put the wig files together in one file by cat? and then use the bigwig program?
2. I tried to follow exaple two and downloaded the wigglefile and the textfile and made the bigwigfile (mybigwig.bw) But I do not understand what to do in the next step (7). I understand this step as adding a line to the bigwigfile, but this is a binary file. So I don't get it.
Thanks
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Old 12-16-2010, 07:02 AM   #2
dawe
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Quote:
Originally Posted by khb View Post
I've used MACS and got one wig file per chromosome. I want to make a bigwig file and used the manual on ucsc http://genome.ucsc.edu/goldenPath/help/bigWig.html.
1. Should I put the wig files together in one file by cat? and then use the bigwig program?
2. I tried to follow exaple two and downloaded the wigglefile and the textfile and made the bigwigfile (mybigwig.bw) But I do not understand what to do in the next step (7). I understand this step as adding a line to the bigwigfile, but this is a binary file. So I don't get it.
Thanks
you have to concatenate your wig files:

Code:
$ zcat *.wig.gz | wigToBigWig -clip stdin chromsizes.tab out.bw
To visualize your bigwig track you have to place it in a location visible by http/ftp protocol and then make the genome browser aware of it by adding this text:

Code:
track type=bigWig bigDataUrl=http://URL/of/out.bw
in the text field you get when you want to add a track.
Unfortunately, if your bw file is not visible by the genome browser (i.e. you are behind a firewall) you won't be able to see it.
d
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