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Old 07-03-2014, 10:02 AM   #19
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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In that case, it would trim all but the first 4 bases. On the other hand, in this case:

40, 40, 40, 2, 2, 2, 40, 40, 40, 40 would trim all but the LAST four bases, because the there are more high-quality bases on the right end than the left end. The result after trimming is always guaranteed to be the largest possible area with an average quality above the threshold, such that no flanking sub-region has average quality below the threshold. Illumina reads typically have lowest quality on the ends and higher quality in the middle, but you can get low quality in the middle if there's a laser failure or air bubbles in the middle of the run. A single bad base in the middle won't cause half the read to be trimmed unless the average quality threshold is set pretty high, but multiple bad bases in the middle will cause either the first or last half of the read to be trimmed to get rid of them.
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