Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bigWig_an error in UCSC genome browser

    Hi all,

    I made a bigWig file from a published ChIP-Seq data using Homer software. And, I uploaded the "trackfileoutput.txt" to UCSC genome browser (on "Paste URLs or data" in Add Custom Tracks). But, I got an error message such as "Error https://dl.dropboxusercontent.com/u/...ucsc.bigWig.bw is not a big wig file").

    The "trackfileoutput.txt" contains the header information that is uploaded as a custom track to UCSC at below;

    track type=bigWig name="tag_forebrain Total Tags = 5.96e+06, normalized to 1.00e+07" description="tag_forebrain Total Tags = 5.96e+06, normalized to 1.00e+07" bigDataUrl=https://dl.dropboxusercontent.com/u/167314749/tag_forebrain.ucsc.bigWig.bw color=15,94,94 visibility=full yLineOnOff=on autoScale=on yLineMark="0.0" alwaysZero=on graphType=bar maxHeightPixels=128:75:11 windowingFunction=maximum smoothingWindow=off

    And as an example, the format of the "tag_forebrain.ucsc.bigWig.bw" is at blow;

    chr1 3000020 3000136 1.45
    chr1 3000197 3000313 2.89
    chr1 3000940 3001056 1.45
    chr1 3001085 3001201 2.89
    chr1 3001741 3001857 1.45
    chr1 3005707 3005823 1.45
    chr1 3008543 3008659 1.45
    chr1 3010571 3010687 1.45
    chr1 3013107 3013190 1.45
    chr1 3013190 3013223 2.89
    chr1 3013223 3013233 1.45

    Does anyone know about this type of issue? Please share your information to resolve my problem. Thank you.

    taehee

  • #2
    That is indeed not a bigWig file.
    It's a bedGraph file.

    A bedGraph file is a text file.
    A bigWig file is the binary version of a bedGraph file.

    UCSC has a command line utility to convert bedGraph files to bigWig files, called bedGraphToBigWig.

    You can also view the bedGraph file in the UCSC Genome Browser, by changing the track type to bedGraph.
    The bigWig files, however, are smaller and indexed, therefore much faster to load and view.

    Comment


    • #3
      Thanks a lot blancha! I've uploaded my file as the bedGraph. But, I have one more question for you.

      To convert bedGraph to bigWig, I've downloaded the bedGraphToBigWig from UCSC. And I run the program;

      Taehyuks-MacBook-Proesktop Taehyuk$ bedGraphToBigWig tag_forebrain.ucsc.bedgraph mm10.chrom.sizes tag_forebrain.ucsc.bigwig

      But, I get an error like at below;

      tag_forebrain.ucsc.bedgraph is not case-sensitive sorted at line 2003164. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again.

      Could you please give me a hint how I can resolve this issue?

      Many thanks!

      taehee

      Comment


      • #4
        The error message could be correct.
        Just check lines 2003163 to 2003165, to determine the problem.

        Code:
        sed -n '2003163, 2003165'p file.bedgraph
        If you see that the only problem is that the chromosomes are not in case-sensitive lexicographical order, just sort them.

        Code:
        LC_COLLATE=C sort -k1,1 -k2,2n file.bedgraph > file_sorted.bedgraph

        Comment


        • #5
          Thank you very much for your helps! Now, everything is fine.
          Last edited by taehee; 11-03-2015, 08:39 AM. Reason: wrong spelling

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM
          • seqadmin
            Recent Advances in Sequencing Analysis Tools
            by seqadmin


            The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
            05-06-2024, 07:48 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 05-24-2024, 07:15 AM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 10:28 AM
          0 responses
          18 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 07:35 AM
          0 responses
          22 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-22-2024, 02:06 PM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Working...
          X