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  • Chip Seq Normalisation Pipelines

    Hi, I am looking for tools or pipelines to normalise ChIP-Seq data that output normalised coverage files e.g. wiggle files for genome visualisation.

    I would like to normalise samples against their control and also to normalise between multiple samples to compare differential binding profiles.

    Most methods of normalisation appear to be built in to tools that output a set of peaks (peakfinders) or regions of differential binding (diffBind, edgeR, DEseq etc) but do not produce a normalised signal for further analysis.

  • #2
    interesting question.. looking forward to some answers.

    that's because I think there is no such normalization..

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    • #3
      You could check out MANorm (http://www.ncbi.nlm.ni(h.gov/pubmed/22424423) and CHANCE (http://genomebiology.com/2012/13/10/R98/abstract) and see if any of them fits your needs.

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      • #4
        I last used this:

        Taslim C, Wu J, Yan P, Singer G, Parvin J, Huang T, Lin S, Huang K. Comparative study on ChIP-seq data: normalization and binding pattern characterization, Bioinformatics, Vol. 25, No. 18. (15 September 2009), pp. 2334-2340

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