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Old 12-19-2008, 09:53 AM   #6
Nix
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Location: SLC, Utah

Join Date: Jun 2008
Posts: 60
Default USeq chIP-seq package

Here's our publication, it's finally out:

http://www.biomedcentral.com/1471-2105/9/523/abstract

And the project web site:

http://useq.sourceforge.net/

I'd like to suggest running a bake off using some simulated spike-in data until real spike-in data becomes available. This was critical for evaluating the methods used in the USeq package. Basically add simulated spikes to real input DNA sequencing data then run your favorite software to call peaks. I'm near getting together a stranded dataset that would be a good first start. Would be nice to sweeten the pot though. Maybe we could get Illumina to throw in an iPod to the winner?
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