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  • petrosul
    Junior Member
    • Feb 2012
    • 2
    #1

    Error message when uploading a file into UCSC genome browser

    Hi. I used QuEST to find peaks in my ChIP-seq data. It looks good, found 4000 peaks with minimum enrichment of 15. But when I try to upload a calls.filtered.bed file into genome browser, I see this error message:
    "File 'ChIP_calls.filtered.bed' - Error line 3536 of custom track: chromStart after chromEnd (-1 > 3)". The other calls file from a different sample uploads into the browser just fine. I tried to rerun QuEST, but still get the same message uploading this file.
    Tags: None
  • GW_OK
    Senior Member
    • Sep 2009
    • 411
    #2
    did you try looking at line 3536 of the bed file?

    Comment

    • ETHANol
      Senior Member
      • Feb 2010
      • 308
      #3
      The UCSC genome browser doesn't like reads that map off the ends of chromosomes or negative numbers. You can run this little script I wrote on your file or since it is so small just open it up with a text editor and fix the offending line.

      http://sourceforge.net/projects/ethanomics/files/bedEndRepair.pl.gz/
      --------------
      Ethan

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