16S copy number correction

Theory behind mothur
1

Hi,

I guess it’s been a while since this topic was last discussed (Gene copy number correction) and since 2011 a number of papers dealing with this have been published (http://www.ncbi.nlm.nih.gov/pubmed/23460914 http://www.ncbi.nlm.nih.gov/pubmed/23133348 among others). It is clear that the difference in number of 16S copies in different taxa can result in a biased description of the microbial community. I get Pat’s point about the changes in relative abundances, but wouldn’t alpha and beta-diversity metrics be biased or just plain wrong? Has anyone used any gene copy number correction tool, such as CopyRighter, the RDP Classifier, the rrnDB or any other tool?

Thanks

2

I have talked with Tom Schmidt (of rrndb) a lot about this and really don’t see a way to do the correction. What is the copy number for the members of the OP10? WHCB1? It seems like you’ll be making up a lot of information that we just don’t have. As much as you correct things you’ll be screwing them up too. I still think that everything is relative even if you have a copy number variation.