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Old 10-30-2012, 04:49 AM   #2
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Location: Boston

Join Date: Nov 2009
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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:

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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