mothur

normalize shared file based on known 16S copy number

Hello, I’d love it if mothur can normalize shared file based on known 16S rRNA copy number (i.e., rrnDB).
It’s something like normalize_by_copy_number.py in PICRUSt
please also see: http://journals.plos.org/ploscompbiol/a … bi.1002743

Thank you!!
Tatsu

Hi,

I have to admit this is a pretty low priority for us for several reasons, especially because it’s difficult to know with any level of certainty what the copy number is for a group of bacteria. What is the copy number for a member of an uncultured phylum? For the Lachnospiraceae? etc. Also, when we are comparing communities, it is done on a relative basis and so if a bacterium goes up or down, so will it’s rrn copies. If you want absolute numbers, you are best off using qPCR on a single copy gene. Thing like normalize by copy number are at best a hack.

Pat