SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to differentiate between PCR duplicates and real data? frymor Bioinformatics 5 09-15-2011 12:05 PM
PCR duplicates questions slny Bioinformatics 8 06-07-2011 03:06 AM
Pico Green vs Real Time PCR crndy52 454 Pyrosequencing 5 02-09-2011 12:18 AM
Picard MarkDuplicates - How to identify duplicates in generated BAM file makarovv Bioinformatics 6 11-10-2010 08:02 AM
how critical is the filtering of potential PCR duplicates? julien General 3 03-26-2010 09:24 AM

Reply
 
Thread Tools
Old 10-26-2012, 02:23 PM   #1
aquleaf
Member
 
Location: Baltimore

Join Date: Mar 2010
Posts: 38
Default 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
aquleaf is offline   Reply With Quote
Old 10-30-2012, 04:49 AM   #2
pbluescript
Senior Member
 
Location: Boston

Join Date: Nov 2009
Posts: 224
Default

Quote:
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

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.
pbluescript is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:33 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO