Hello Folks,
Wanted to point folks running chIP-seq analysis to http://sourceforge.net/projects/useq/ . Be sure to hit the 'Project Web Site' button for more information. It contains 25+ command line java applications for both low and high level analysis. We have developed several statistics to minimize false positives using control input data and assign confidence in the peaks via empirical FDRs, binomial p-values and q-values.
Also wanted to recommend folks check out the Integrated Genome Browser and it's use of DAS/2 for distributing public/ private chIP-seq data. It's the only viable solution I've so far encountered. See http://bioserver.hci.utah.edu/BioInf...p/Software:IGB .
-cheers, David
Wanted to point folks running chIP-seq analysis to http://sourceforge.net/projects/useq/ . Be sure to hit the 'Project Web Site' button for more information. It contains 25+ command line java applications for both low and high level analysis. We have developed several statistics to minimize false positives using control input data and assign confidence in the peaks via empirical FDRs, binomial p-values and q-values.
Also wanted to recommend folks check out the Integrated Genome Browser and it's use of DAS/2 for distributing public/ private chIP-seq data. It's the only viable solution I've so far encountered. See http://bioserver.hci.utah.edu/BioInf...p/Software:IGB .
-cheers, David
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