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Old 01-29-2015, 11:30 AM   #6
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
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By default, BBNorm will run 2 passes. The first pass will normalize to some depth higher than the ultimate desired depth, and the second pass will normalize to the target depth. This allows, in the first pass, preferential discarding of reads that are low quality. So the result from the second pass should still be a target of 10x.

You can instead set "passes=1" which will aim for the target on the first pass and not do a second pass. This is slightly faster but will typically yield data with more errors. Neither is universally better, though.

If you are going to target a depth of 10x, it's important to also reduce "mindepth" - by default it is 6, which is appropriate for 40x but not for 10x. Probably 2 would be better. Everything with apparent depth below that gets discarded.
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