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  • schaffer
    Member
    • Apr 2009
    • 12
    #1

    BEDtools: genomeCoverageBED

    Hi,
    I need to confirm that using the -bg option to create a bedgraph will indeed
    make a track in UCSC browser which uses the count information in the 4th column? The annotation for bedgraph in UCSC website does not specify any specific data for this column and we need to see the count data per bp position in the track (histogram).
    genomeCoverageBed -bg -trackline -trackopts name=${new} -i $file -g sizeMouse.txt > ${new}.bedgraph

    chr6 3323588 3323615 1
    chr6 3323696 3323710 1
    chr6 3323710 3323721 2
    chr6 3323721 3323730 3
    chr6 3323730 3323741 2
    chr6 3323741 3323790 3
    chr6 3323790 3323799 2
    chr6 3323799 3323800 1
    Thanks for any insight,
    Lana
    Tags: None
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