View Single Post
Old 05-19-2015, 10:29 AM   #16
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

To expand upon that, BBMap has the options for internally quality-trimming (and untrimming) reads, but I only use them in special cases. For example, BBMap is used a lot for filtering out contamination. To ensure high specificity, I only want to remove reads that map to contaminant sequences with high identity; but I don't want the identity calculation to include low-quality bases. So, I map with "qtrim=rl trimq=15 untrim" or similar, which will trim before mapping but then output the untrimmed read.

For normal cases such as variant calling or coverage calculation, don't quality-trim unless you have really low quality data. I would not expect that to be the case for a 100bp library.
Brian Bushnell is offline   Reply With Quote