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Distinguish real duplicates from those generated by PCR

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  • Distinguish real duplicates from those generated by PCR

    Hi All.

    Sorry to bother you. Is there a way to distinguish duplicates caused by high sequencing depth from the PCR artefacts?

    One more question. Is it necessary to remove the duplicates in the transcription factor ChIP-Seq? In our TF ChIP-Seqs, It is often to see a high duplication level. It is not the case in the controls. I guess the duplicate is caused by high sequencing depth not by the PCR artefacts.

    Wish your help! Thanks very much!


    Best, Mei

  • #2
    Originally posted by aquleaf View Post
    Sorry to bother you. Is there a way to distinguish duplicates caused by high sequencing depth from the PCR artefacts?
    Only if you added a unique barcode to each individual molecule during library prep before PCR. There are a couple papers out there that have done this. Here's one example:
    http://nar.oxfordjournals.org/conten...ar.gkr217.long

    One more question. Is it necessary to remove the duplicates in the transcription factor ChIP-Seq? In our TF ChIP-Seqs, It is often to see a high duplication level. It is not the case in the controls. I guess the duplicate is caused by high sequencing depth not by the PCR artefacts.
    I would not remove any potential duplicates from ChIP-Seq data. You are sampling from a smaller portion of the genome, so duplicates are expected.

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