sub.sample selectively?

Commands in mothur
#1

Hi,

I have a dataset where the sequences come from very different sources, but I’d like to analyze all of them together, at least for beta-diversity.
When I get to count.groups the dramatic differences in source material cause dramatic differences in number of sequences per group. Can I sub.sample separately for each source, using key identifiers in the sampleName for each?

i.e., I have 14 groups/samples whose sample name start with “Az_”–can I subsample these to 600, but subsample the 4 groups/samples whose sample name starts with “Coc_” to 1500?

Many thanks,
Beth

#2

No. To do what you want to do, you’d have to do get.groups on the shared file and subsample the separate subsampled shared files. I’m not sure I can think of a case where you’d want to do an analysis where things would be subsampled differently.