normalize shared file based on known 16S copy number

Feature requests
1

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

2

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