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  • visualise co-occupy of a genome with bed files

    Hi,

    we have some mouse chip-seq data from 4 transcription factors (TFs) that we can look for possible binding sites or target genes for each TF.

    Interestingly we found many binding sites overlaps among the 4 TFs by UCSC browser, however, UCSC browser cannot draw the whole picture of co-occupy of the genome with these 4 TFs data. A good example would be this Figure 1C (http://www.ncbi.nlm.nih.gov/pmc/arti...730/figure/F1/ . But it does not mention how to generate the picture.

    Can anyone suggest a method to visualise the co-occupy of a genome (overlaps) from several Bed files from chip-seq experiments please?

    many thanks.

  • #2
    I don't know about visualization, but the UCSC Table Browser can output overlaps between tracks, so if you load the bed files it can output a list of where they overlap. Bedtools can also quickly find overlaps and output a list of positions, but I think it's just pairwise so you'd have to run it a few times to find somewhere that overlaps in 4 sets.

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    • #3
      hi, biznatch.

      thanks for the quick reply, I did try table browser, as you suggested, I can get the overlap list from this, or from BEDTools kit.

      What we really want to show is the overall overlap Figure in the mouse genome, the detailed interesting overlap binding sites are discussed individually somewhere else.

      Presumably there are some R package for plotting can do the job, but not sure.

      cheers

      middlemale

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