Hi,

If you are aligning against a reference genome, I don't think you really need to do this.

In my experience, you don't need to filter low-quality bases for splicing or differential expression analysis.

I've mainly worked with read lengths of 50 bases or more and genomes where 99% of introns are 5 kb or smaller. So this advice may not to apply to your case.

Best wishes,

Ann

-------------------------------

Ann Loraine, Ph.D.

Associate Professor

Department of Bioinformatics and Genomics

University of North Carolina at Charlotte

North Carolina Research Campus

600 Laureate Way

Kannapolis, NC 28081

704-250-5750

aloraine@uncc.edu

http://www.transvar.org

http://www.bioviz.org

http://www.uncc.edu

From: "Du, Jianguang" <jiandu@iupui.edu>
Date: Thu, 23 Aug 2012 14:48:29 +0000
To: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Subject: [galaxy-user] What is the minimum Quality should I set for Filter FASTQ?

Dear All,

I am analysing RNA-seq datasets for differential splicing events between cell types.

Some of my reads contain bed nucleotides, should I run Filter FASTQ to remove these "not so good" reads? If I do need to, what is the "Minimum Quality" should I set for the Filter?

Thanks.

Jianguang