Unconfigured Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • khb
    Member
    • Dec 2010
    • 15

    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
  • dawe
    Senior Member
    • Apr 2009
    • 258

    #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

    Comment

    Latest Articles

    Collapse

    • SEQadmin2
      Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by SEQadmin2


      I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.


      Here are nine questions we think about, in roughly the order they matter, before...
      Today, 07:11 AM
    • SEQadmin2
      From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
      by SEQadmin2


      Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.


      The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
      ...
      06-02-2026, 10:05 AM
    • SEQadmin2
      Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends
      by SEQadmin2


      With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.


      Introduction

      Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
      05-22-2026, 06:42 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by SEQadmin2, Yesterday, 06:09 AM
    0 responses
    16 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 06-09-2026, 11:58 AM
    0 responses
    37 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 06-05-2026, 10:09 AM
    0 responses
    42 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 06-04-2026, 08:59 AM
    0 responses
    49 views
    0 reactions
    Last Post SEQadmin2  
    Working...