relative abundance in original samples

First of all, thanks for providing such a fantastic resource for 454 data analysis!
I’ve managed to work my way through the example analyses on my data set (I’ve used the Costello stool analysis as a guide). I have successfully produced a taxonomy file that describes the taxonomy of the OTUs in the processed data. However, I’d like to know the relative abundance of specific OTUs in my original data set (which contains 13 samples, 4 locations x 3 reps and 1 location x 1 rep).
Essentially I’d like to know how the relative abundance of SRBs (for example) alters between locations. As far as I can see the summary file produced by classify.seqs with the groups option produces data that describes how the unique sequences are distributed across my samples. I’d like an equivalent data set for all good (but not unique) sequences.

Thanks for helping out a newbie
Steve R

Steve -

I think what you need to check out are the get.relabund and metastats commands… let us know if you have any problems.


Many thanks. I’ll give it a go.