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wiggle or bedGraph

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  • wiggle or bedGraph

    Hi all,

    I have about 300,000 lines of data I want to add to UCSC genome browser as a custom track.

    Few lines of the data I have are:
    =======
    Chr Start End Count_1 Count_2 p-value
    chr1 16672622 16899459 11 10 0.660251747
    chr1 99208070 99248356 19 30 0.660962498
    chr3 90321218 90321465 12 1 0.661320514
    chr3 92621688 92658292 4 1 0.662124217
    =======

    As I have start and end coordinates, it seems natural to use bedGraph format for this 300,000 lines of data using the coordinates and p-value. But the problem is that I want to display Count_1 and Count_2 too. Is there a way that I can display more than one data associated with a given coordinates in UCSC browser? I thought of making three different custom tracks but the resulting image didn't seem right.

    If it is not possible with bedGraph format, is it possible to do such thing (displaying more than one data associated with a given location) with Wiggle or any kind of format that UCSC will understand?

    Thank you,
    Statsteam

  • #2
    just curious --- why didn't the images "seem right?"

    I'm not an expert, but I can't think of any other way than multiple bedGraph tracks. If it helps, you can do more complex intersection and other kinds of queries using Galaxy, which you can get to from the genome browser ...

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    • #3
      I was struggling a bit while displaying big tracks in UCSC Gbrowser. I found a better option to use the IGV genome browser than working remotely. I'd suggest the community to have a look on it.

      http://www.broadinstitute.org/igv/

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      • #4
        From http://www.broadinstitute.org/igv/do...rmats_TEXT.htm

        IGV File Format

        An IGV file (.igv) is a tab-delimited text file that defines tracks. The first row contains column headings for chromosome, start location, end location, and feature followed by the name of each track defined in the .igv file. Each subsequent row contains a locus and the associated numeric values for each track. For example, this .igv file describes three tracks:
        Chromosome Start End Feature Patient-One Patient-Two Patient-Three
        chr1 2150459 2150460 Test_one 0.01 0 0.99
        chr1 3558044 3558045 Test_two 0.25 0.71 1.31



        Note: Data must be grouped by chromosome. One easy way to do this is to sort by start location.

        IGV interprets the first four columns as chromosome, start location, end location, and feature name regardless of the column headings in the file. IGV uses the column headings for the fifth and subsequent columns as track names. Feature names (the values in the fourth column) are not displayed in IGV.

        IGV displays IGV-formatted files with generic default track display settings that may not provide enough visual detail. To cause IGV to display an IGV-formatted file with more helpful display settings, you can:

        * Include a #type line in the file to make IGV use the display settings for a different data type (for example, the GCT data type). See Changing the Default Track Display Settings for a Data File.
        * Specify default display settings by including a WIG track line in the file: See WIG File Format for information on the syntax and specifiers to use in this line. In the IGV file format, the track line must begin with a # symbol. (This is an IGV-specific constraint on IGV-formatted files. WIG file track lines do not require the # symbol.)

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