SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
The NEXTflex™ PCR-Free DNA Sequencing Kit Reduces Bias in NGS Library Prep Bioo Scientific Vendor Forum 10 12-20-2012 07:10 AM
PCR primer -- a PCR simulation on your computer gringer General 0 01-26-2012 02:03 AM
dealing with 5' end bias in RNASEQ PFS Bioinformatics 4 09-06-2011 10:27 PM
PCR bias by backfolding amplicons Sebastian123 Sample Prep / Library Generation 3 02-09-2011 03:10 AM
Number of PCR How many PCR cycles to enrich adapter-modified DNA fragments MGH Man Sample Prep / Library Generation 5 07-26-2010 05:15 AM

Reply
 
Thread Tools
Old 10-19-2011, 01:11 PM   #1
schaffer
Member
 
Location: San Diego

Join Date: Apr 2009
Posts: 12
Default RNASeq removing PCR bias

Hi,
What is the best way to remove PCR bias in RNA-Seq? Is deleting all reads that map to the same start and stop position except the best quality read a good solution?
Lana
schaffer is offline   Reply With Quote
Old 10-19-2011, 01:32 PM   #2
jwfoley
Senior Member
 
Location: Stanford

Join Date: Jun 2009
Posts: 181
Default

The best way is to reduce the number of PCR cycles. Deleting "duplicate" reads is a very bad solution if you want do any kind of quantitative analysis. Here is a previous discussion on that topic: http://seqanswers.com/forums/showthread.php?t=6543
jwfoley is offline   Reply With Quote
Old 10-20-2011, 02:47 PM   #3
cedance
Senior Member
 
Location: Germany

Join Date: Feb 2011
Posts: 108
Default

You should check this post. Its one of the best discussions I have read.
http://seqanswers.com/forums/showthread.php?t=6854

Especially replies by malachig, kmcarr and lh3.
cedance is offline   Reply With Quote
Old 10-20-2011, 06:00 PM   #4
Dario1984
Senior Member
 
Location: Sydney, Australia

Join Date: Jun 2011
Posts: 166
Default

Fragment duplication is just one kind of PCR bias. Base content is another.
Dario1984 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 09:39 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO