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Old 11-16-2015, 12:31 PM   #4
Brian Bushnell
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Location: Walnut Creek, CA

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You shouldn't error-correct if you are looking for rare variants (much less than the 50% ratio of a normal heterozygous diploid variant), or are doing amplicon sequencing, or are looking at tumor samples, or you have low coverage. Also, error-correction won't help much with platform-specific errors (like being unable to correctly determine the length of a long homopolymer), just with random errors.

If you have a reference, you can map before and after error-correction, and look at the error rates, to make sure error-correction improved things.
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