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Old 05-19-2015, 10:29 AM   #16
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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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.
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