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  • Running NPS (nucleososme positioning from Seq) on Chipseq data

    I have a kind of basic question- I have a SE chipseq data for histone modification, Do we need to a specific wet lab experiment before we run NPS alogrithm for checking nucleosome positioning. The data I have is from regular chipseq and is not specifically from nucleosome fraction. My idea is to overlay the histone modification regions with nucleosome positioning. Any suggestion or feedback please.

  • #2
    Is your data MNase digested or fragmented by sonication?

    I know that if you have H3k4me3 MNase seq, the position of individual nucleosomes can be visualized, but with sonication you just get a blob of a signal over the TSS.

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    • #3
      nucleosome position from regular chipseq

      It is a variant of H2AZ and the samples are just sonicated and are not MNase digested.

      Thanks

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      • #4
        I somehow doubt that the NPS will give you the results you want. I tried doing the nucleosome prediction on my H3k4me3 and H2A.z sonicated samples, and the results were almost random. If you really want the true resolution, I would recommend you to do the MNase experiment with the histone.

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