remove the singletons using remove.rare in mothur
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6.2 years ago

Can you please advise if the following steps will do the job? Many thanks. If not, could you please also give us some suggestions (especially which commands should be used, and at which steps). Thanks.

I did these: Following mothur SOP,
1. mothur > sub.sample(shared=stability.an.shared, size=6105) Sampling 6105 from each group. 0.03

Output File Names: stability.an.0.03.subsample.shared

  1. mothur > remove.rare(shared=stability.an.0.03.subsample.shared, nseqs=1) 0.03

Output File Names: stability.an.0.03.subsample.0.03.pick.shared

  1. mothur > count.groups(shared=stability.an.0.03.subsample.0.03.pick.shared) Total seqs: 207161.

Output File Names: stability.an.0.03.subsample.0.03.pick.count.summary

Get the minimal number of OTUs that were present in all of these samples, then go from there for : collect.single(shared=stability.an.0.03.subsample.0.03.pick.shared, calc=chao-invsimpson, freq=100)

Does this insertion make senses? I mean, if I want to compare the results with (these procedures) and without the removing the singletons (by using the original mothur SOP).

Have a great day!

next-gen sequencing • 2.1k views
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