Which soft is better for very broad ChIP-Seq enrichments (~1000 - 1000000 bp)

[rebrendi]

Hello,

Any suggestions with respect to a specific software, or a specific set of parameters for a standard software, to identify very broad regions of ChIP-Seq enrichments (~1000 - 1000000 bp)?

Thanks!

[A Oshlack]

Have you tried Zinba? They say it can do that although I haven't tried it myself.

http://genomebiology.com/2011/12/7/R67

[Richard Finney]

cisgenome :http://www.biostat.jhsph.edu/~hji/cisgenome/

Spotty documentation and cryptic error messages ... (what's new in the world of free software for bioinformatics?) ... but seems pretty solid. I only used the command line versions (for use with Linux/Cygwin/Apple) but they say they have a Windows GUI.