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  • any software to draw gene track together with ChIP-seq peak

    Hi all,

    Do you know any software can draw gene tracks with ChIP-seq peak at an individual gene?

    Thanks!

  • #2
    Also, it will be great if the browser can display long- range interaction data like Hi-C and ChIA-PET data

    Comment


    • #3
      If you have a BED format file with the necessary peak location information available then most of the genome browsers (UCSC, IGV, Ensembl) can display this information (provided your genome is available).

      Comment


      • #4
        Originally posted by GenoMax View Post
        If you have a BED format file with the necessary peak location information available then most of the genome browsers (UCSC, IGV, Ensembl) can display this information (provided your genome is available).
        Thanks, I use UCSC genome browser a lot, but I prefer a local genome browser like IGV.

        I know IGV can do the job for ChIP-seq data.

        I have a wig file for the ChIP-seq data, I also have a ChIA-PET data set. I want to display them together. can IGV display ChIA-PET data with format something like this:

        chr1 1000 2000 chr1 5000 6000 7

        first three columns are the position of one end and the following three columns denoting
        the position of the other end. the last column denotes the tag number of the interaction found in the experiment.

        Comment

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