sub.sample for denoised data


I have a pyrosequencing run with vey different amounts of sequences from different samples. I have denoised the sequences, but would now like to “subsample” so I can directly compare the diversity in the different samples. Can I do this on denoised sequences using the sub.sample command? How would this work? Does this command work the same way as “daisy chopper”?
Also, if the answers to this is “no”, any suggestions on how I should do this would be appreciated!


Best, Sonja

Have you looked at

It would probably be best to run it on a shared file.