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-   -   Distinguish real duplicates from those generated by PCR (http://seqanswers.com/forums/showthread.php?t=24482)

aquleaf 10-26-2012 02:23 PM

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

pbluescript 10-30-2012 04:49 AM

Quote:

Originally Posted by aquleaf (Post 87810)
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

Quote:

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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