Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

  • #2
    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/

    Comment


    • #3
      thanks a lot!

      Originally posted by lparsons View Post
      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/
      Thank you, that's great help!

      Comment


      • #4
        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. —Aristotle

        Comment


        • #5
          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...

          Comment


          • #6
            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.

            Anthony
            The more you know, the more you know you don't know. —Aristotle

            Comment


            • #7
              Thank you all very much!

              Comment


              • #8
                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, David

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Exploring the Dynamics of the Tumor Microenvironment
                  by seqadmin




                  The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                  07-08-2024, 03:19 PM
                • seqadmin
                  Exploring Human Diversity Through Large-Scale Omics
                  by seqadmin


                  In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                  06-25-2024, 06:43 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Today, 07:20 AM
                0 responses
                16 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-16-2024, 05:49 AM
                0 responses
                35 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-15-2024, 06:53 AM
                0 responses
                39 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-10-2024, 07:30 AM
                0 responses
                41 views
                0 likes
                Last Post seqadmin  
                Working...
                X