[mudshark]

@mudshark. You've tried quite a few programs. More than I have. Since I use QuEST the most could you tell me why you think it doesn't perform well? Did you use default or advanced parameter settings? This paper found most peak-calling programs to have high agreement between high-value peaks and qPCR verification data http://www.plosone.org/article/info:...l.pone.0011471

based on my prior-knowledge system i can do a very good performance estimation of the tools. basically i know all the binding sites genome-wide without having to do ChIP mappings.

of course, I am working in Drosophila and QuEST e.g. has been 'optimized' for mouse/human whatever that means. but in essence, QuEST has a very low sensitivity and given the low sensitivity a rather bad specificity COMPARED to other tools such as SICER, spp, and MACS.

my experience.. other people might have a different one.

(and of course i find QuEST very poorly documented - what are the advanced parameters?)

[captainentropy]

mudshark, if you include the "-advanced" option in the QuEST command you will have the option to configure all of the parameters such as bandwidth, region size, mappable genome fraction, ChIP enrichment, peak shift, etc. You can also control the peak collapsing parameters too.

I recommend using the advanced option and at a minimum change the mappable genome fraction to something more accurate. The fraction is a function of the read length and percentage of mappable sequence (i.e. the non-repetitive sequences) for your genome. The longer the read length the larger the mappable fraction. The default in QuEST is 0.75 which (for hg18) corresponds to a readlength of 26nt. We are getting read lengths of 38nt and longer which increases the fraction to 0.82 and up. Using this number has resulted in a noticeable increase in number of peaks called.