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Old 02-11-2014, 06:23 AM   #1
lisa.brown
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Question Rarefaction

Is it unacceptable to remove chimeras, shorter than expected reads, and low q-score reads prior to doing a rarefaction analysis? I'm working with 454 16S data and it just makes sense to remove this kind of data from each library prior to alignment and clustering. I've been questioned on my method that told that rarefaction analysis should be calculated on raw data. Thoughts?

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Old 02-11-2014, 06:41 AM   #2
dpryan
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Would you have used those reads anyway for downstream analyses? If not, then I would find it difficult to argue against removing them.
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Old 02-11-2014, 07:53 AM   #3
lisa.brown
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Great! That's my reasoning as well, the removed reads WOULDN'T be used for downstream analysis so why produce rarefaction data that isn't comparable to downstream hierarchy data?
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