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  • Correlating/clustering RNA-seq with ChIP-seq data?

    Hi everyone,

    I have RNA-seq data from adipocytes, where a certain gene, that is involved in heterochromatin, is knocked out. I would like to correlate/cluster this dataset with another dataset, where we have ChIP-seq for H3K9me3.

    Basically, I would like to see if those genes that are upregulated in my knockout samples are the one that are enriched for H3K9me3.

    I have tried to search the forum here and have read several posts about the topic, but I am still not sure how to go about it and what packages to use.

    Thanks a lot! Appreciate your help.

    // Kevin

  • #2
    I know the TargetCaller package for R, but this is mainly for transcription factors. Whether it is suited for Histon ChIP-data you have to test.

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    • #3
      Have a look at the "Integrative analysis of epigenetics and gene expression" section of the Repitools manual. The heatmap plot is what you want to use.

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      • #4
        There's also the Rcade package in Bioconductor (R-based analysis of ChIP-seq And Differential Expression)...

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