make.shared

dong5600 · April 10, 2014, 8:47pm

Hi, Pat:

When running make.shared, no matter which cutoff I chose, I only got results for unique and/or 0.01, but I need 0.03 cutoff. Can you give me some suggestion? Thanks a lot!

Below is some of the examples:

mothur > make.shared(list=Calgary.unique.good.filter.unique.precluster.pick.an.list, group=Calgary.good.pick.group, label=unique-0.01-0.03)

unique
0.01

Output File Names:
Calgary.unique.good.filter.unique.precluster.pick.an.shared
Calgary.unique.good.filter.unique.precluster.pick.an.MCB010_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB010_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB012_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB012_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB013_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB013_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB016_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB017_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB017_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB018_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB018_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB01_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB01_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB02_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB02_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB03.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB04_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB04_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB05_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB05_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB06_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB06_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB08_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB08_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB09_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB09_2.rabund

mothur > make.shared(list=Calgary.unique.good.filter.unique.precluster.pick.an.list, group=Calgary.good.pick.group, label=0.03)

0.01

Output File Names:
Calgary.unique.good.filter.unique.precluster.pick.an.shared
Calgary.unique.good.filter.unique.precluster.pick.an.MCB010_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB010_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB012_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB012_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB013_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB013_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB016_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB017_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB017_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB018_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB018_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB01_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB01_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB02_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB02_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB03.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB04_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB04_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB05_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB05_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB06_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB06_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB08_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB08_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB09_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB09_2.rabund

mothur > make.shared(list=Calgary.unique.good.filter.unique.precluster.pick.an.list, group=Calgary.good.pick.group, label=0.1)

0.01

Output File Names:
Calgary.unique.good.filter.unique.precluster.pick.an.shared
Calgary.unique.good.filter.unique.precluster.pick.an.MCB010_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB010_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB012_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB012_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB013_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB013_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB016_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB017_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB017_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB018_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB018_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB01_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB01_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB02_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB02_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB03.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB04_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB04_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB05_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB05_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB06_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB06_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB08_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB08_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB09_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB09_2.rabund

mothur > make.shared(list=Calgary.unique.good.filter.unique.precluster.pick.an.list, group=Calgary.good.pick.group)
unique
0.01

Output File Names:
Calgary.unique.good.filter.unique.precluster.pick.an.shared
Calgary.unique.good.filter.unique.precluster.pick.an.MCB010_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB010_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB012_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB012_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB013_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB013_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB016_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB017_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB017_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB018_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB018_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB01_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB01_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB02_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB02_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB03.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB04_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB04_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB05_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB05_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB06_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB06_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB08_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB08_2.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB09_1.rabund
Calgary.unique.good.filter.unique.precluster.pick.an.MCB09_2.rabund

pschloss · April 11, 2014, 12:49pm

How are you running dist.seqs and cluster (or cluster.split)?

You might check out this FAQ:

http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F

Ghazal · July 30, 2015, 12:01pm

Hello
I have used make.shared after cluster.split on in total 2,770,000 sequences (10,000 sequences per each 277 persons) and 210166 unique sequences. It resulted in 94,776 OTUs. Could it be correct? How many OTUs do we expect to have for these number of reads? Is there a rule of thumb for it?
Many thanks in advance.

pschloss · August 3, 2015, 2:44pm

That might be reasonable, I’m not sure. Do you know what your error rate is from sequencing a mock community in parallel to your samples? You may also want to consult this post:

http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/

Pat

Ghazal · August 3, 2015, 3:26pm

Thanks a lot
I have already read it
Unfortunately, we don’t have any mock community. Isn’t there any rule of thumb for it? I mean a hypothetical ratio between the number of sequences or unique sequences and the number of OTUs we can reasonably have?
Many thanks for your kind help

Ghazal

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