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.



  • 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