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  • High duplication rate for INPUT (ChIP-seq)

    Hi all,

    I am analysing ChIP-seq data and got very noisy output except for the histone mark H3K4me3. The others marks (H3K9me3 and H3K9ac) and particularly the input samples got high rate of duplicates reads (up to 75% for the input).

    To what I understand I should have the lower duplicate rates for the input samples as it should be of high diversity?!

    I started with 10ng of DNA for all the samples and used the Illumina ChIP protocol as indicated.

    As the ChIP-q-PCR showed enrichment, I am wondering if something could have happens during the library prep.

    Any advice is welcome!!

    Thank you for your help!

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