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-   -   convert wig to bigwig (http://seqanswers.com/forums/showthread.php?t=8448)

khb 12-16-2010 05:22 AM

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. :confused:
Thanks

dawe 12-16-2010 08:02 AM

Quote:

Originally Posted by khb (Post 31525)
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. :confused:
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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