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MACS wig files on UCSC?

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  • MACS wig files on UCSC?

    Dear all,

    I got wig files for each chromosome from MACS peak calling output. Instead creating a custom tract for each chromosome, is there a way to join them into a single file and view it on UCSC genome browser? I googled around for a bit without success, it would be great if you could provide some help. Thanks!

  • #2
    Originally posted by yh253 View Post
    Dear all,

    I got wig files for each chromosome from MACS peak calling output. Instead creating a custom tract for each chromosome, is there a way to join them into a single file and view it on UCSC genome browser? I googled around for a bit without success, it would be great if you could provide some help. Thanks!
    Code:
    zcat *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig

    Comment


    • #3
      Hi, I would also be interested in knowing how to do this. The above command fails with the following message:

      Unrecognized line 7123307 of stdin:
      track type=wiggle_0 name="[PATH]/[FILE]" description="Extended tag pileup from MACS version 1.4.2 20120305 for every 10 bp"

      Thanks!

      Comment


      • #4
        Originally posted by albireo View Post
        Hi, I would also be interested in knowing how to do this. The above command fails with the following message:

        Unrecognized line 7123307 of stdin:
        track type=wiggle_0 name="[PATH]/[FILE]" description="Extended tag pileup from MACS version 1.4.2 20120305 for every 10 bp"

        Thanks!
        You can try

        Code:
        zgrep -hv 'track' *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig

        Comment


        • #5
          Hi, I have the same problem. The -clip option did not help.

          ./wigToBigWig track1034.wig hg18.chrom.sizes track1034.bigwig
          Unrecognized line 97361 of track1034.wig:
          track type=wiggle_0 name="MACS_treat_chr13" description="Shifted Merged MACS tag counts for every 25 bp"

          ./wigToBigWig -clip track1034.wig hg18.chrom.sizes track1034.bigwig
          Unrecognized line 97361 of track1034.wig:
          track type=wiggle_0 name="MACS_treat_chr13" description="Shifted Merged MACS tag counts for every 25 bp"

          Comment


          • #6
            The -S option will works.

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