Brandon:LabNotes/Project1/2012-2-16
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Peakseq, peak calling programs[edit]
- search "chip seq peak calling" on pubmed
- latest algorithm to be developed at this time is peakROTS, which is compare to peakseq and MACS. peakROTS, latest peak caller
- Though only has negligible improvement over other methods, maybe will try out later.
- peakseq, MACS, FindPeaks, USeq comparison Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data
- Peakseq is least stringent and will call some false positives, while MACS is most stringent and will not call some significant peaks. validation with ChIP-PCR.
- can use both peakseq and MACS to determine significance of lesser peaks.
- comparison between 11 programs. Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
- conclude they have comparable performance, comment that improvement in algorithms will provide little improvement in peak calling in terms of sensitivity. Should focus on doing replicates for comparison, and sound preparation methods.
conclusions[edit]
- peakseq is good, others have comparable performance and don't need to be improved upon.
- will try MACS