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<mailto:jiandu@iupui.edu>> Date: Thu, 23 Aug 2012 14:48:29 +0000 To: "galaxy-user@lists.bx.psu.edu<mailto:galaxy-user@lists.bx.psu.edu>" <galaxy-user@lists.bx.psu.edu<mailto: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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/