Annotating Genomic Intervals

[turnersd]

(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.

[kadircaner]

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..