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  • Problem to display wig files on UCSC.

    Hello everyone,

    Since the arrival of TopHat2 I completely abandoned the use of TopHat1. The problem is that the "Wiggles" tool of TopHat does not exist for TopHat2. (In addition, the Wiggles tool was very slow). So I use IGVtools count, now, to generate my wig files. The problem is that the wig files are displayed in the IGV tool but not in the UCSC genome browser. Yet I have no error when uploading wig files in UCSC. But the data does not appear, the frame corresponding to the file remains empty. I can not find solutions to my problem.

    Wig file I use :


    track type=wiggle_0 name="sample_name" description="description" visibility=full alwaysZero=on windowingFunction=maximum
    variableStep chrom=chr1 span=10
    14371 1.8
    14381 2
    14391 2
    14401 2
    14411 1.8
    14891 1
    14901 1.6
    14911 3.7
    14921 5.1
    14931 5.8
    14941 5
    14951 4.4
    ...
    ...
    ...
    variableStep chrom=chr10 span=10
    96331 1
    96341 1
    96351 1
    96361 1
    97191 1
    97201 1
    97211 1.5
    97221 2
    97231 2
    97241 1
    97251 1
    97341 2
    97351 2.9
    ...
    ...
    ...
    Someone used IGVtools to generate these wig files? You encounter this problem?

    And if not, what tool you used to generate wig file for RNA-seq data?

    Thank you in advance for your help.

  • #2
    Originally posted by velt View Post
    Yet I have no error when uploading wig files in UCSC. But the data does not appear, the frame corresponding to the file remains empty. I can not find solutions to my problem.
    I think this means your upload is timing out. If your file take too long to upload and/or is over 500MB you'll have to convert it to bigwig and put it on a server. In my experience if you're over 500MB you'll get an error message but if it's taking too long you just get the blank screen with no error.

    Comment


    • #3
      Thank you for your reply !
      This is not a timeout problem. Indeed, my file weighs only 300 MB.
      And even when I split into four equal sized files, and I want to upload these files to UCSC, I have no error and data not be displayed.

      Comment


      • #4
        How long are the files uploading for before you get the error/blank screen? 300MB should be fine as long as your upload speed is fast enough to upload within the required time limit (which is a few minutes I think).

        Comment

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