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  • chip-seq cluster,s number

    Hi

    I am doing my first chip seq analysis. I have an issue with my samples, the cluster numbers are a lot lower than I would want. The cluster numbers range from 29k to 69k for these samples and for others range from 132-145k.
    However I guess it all depends on peaks vs. background,

    I m wondering if I can get good data from ~50k clusters ?

    I'm not familiar with how the analysis is done though.

    Please f someone can help me with understanding what does mean the cluster number, what can have an effect on the number of clusters?

    Thank you very much for help, Gio

  • #2
    What software you used to get the clusters?
    Xi Wang

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