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  • 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

  • #2
    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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