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  • Annotating Genomic Intervals

    (Cross-posting from Biostars):

    How can I annotate human genomic intervals (BED file) from a ChIP-seq experiment with information such as: Does the interval overlaps with a gene(s)? Which gene(s)? Upstream of a gene? Overlaps with an exon? Intron? 5kb upstream/downstream of TSS? Intergenic? Perhaps more difficult - does it overlap with a DNAse I hypersensitive site?

    Surely bedtools/intersectBed can help me with this, but I'm looking for the best workflow / data sources to use for this that will require the least amount of scripting.

    Thanks.
    Last edited by turnersd; 10-01-2012, 09:41 AM. Reason: fixed link to biostar

  • #2
    You can try GREAT(great.stanford.edu) or CEAS (from Liu Lab @Harvard) but none of those can tell you about DNAse sites I believe..

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