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  • #1

    Softwares/Pipelines for ChIP Seq Analysis

    Hi,

    I have been working on the ChIP Seq data for a year now. I have been using software like SPP, MACS, Quest for peak detection. I would like to know which "freely available" ChIP Seq software you use and why ?

    Also, do you choose one software over other depending upon the cell type that you are using. I have read a couple of software and it seems that SPP and MACS have been the most popular one but the common problem that I have seen is when a version of MACS comes sometimes it does not gives the same output as given by the previous version.

    Any advice or suggestions will be highly appreciated.

    Thanks.
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