# Cluster command output

**URL:** <https://forum.mothur.org/t/cluster-command-output/1114>\
**Category:** Commands in mothur\
**Created:** [November 6, 2012, 4:38pm UTC](https://forum.mothur.org/t/cluster-command-output/1114 "2012-11-06T16:38:49Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![miguelangel](https://avatars.discourse-cdn.com/v4/letter/m/e8c25b/32.png) [@miguelangel](https://forum.mothur.org/u/miguelangel)\
**Post date:** [November 6, 2012, 4:38pm UTC](https://forum.mothur.org/t/cluster-command-output/1114/1 "2012-11-06T16:38:49Z")

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Hello there.

I am working with the Schloss SOP with my own sequences and I have a problem:

After running my ‘dist.seqs’ and my ‘cluster’ commands in order to find OTUs present in my fasta I get 3 files: .sabund, .rabund and .list.

How could I get a .fasta file with my cluster at 0.03, for instance? I do not want only the sequences name, but also the nucleotide sequence itself for the representatives of each OTU.

Is it possible?

Thanks a lot

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [November 6, 2012, 7:13pm UTC](https://forum.mothur.org/t/cluster-command-output/1114/2 "2012-11-06T19:13:04Z")

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try get.oturep

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**Author:** ![dwaite](https://avatars.discourse-cdn.com/v4/letter/d/ecccb3/32.png) [@dwaite](https://forum.mothur.org/u/dwaite)\
**Post date:** [November 6, 2012, 7:37pm UTC](https://forum.mothur.org/t/cluster-command-output/1114/3 "2012-11-06T19:37:20Z")

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Something I’ve been wondering for a while - going the OTU-based approach in the SOP you create OTUs at various scales (say 97% similarity) and perform the downstream analysis based on that, but for a phylogenetic approach it seems to just be at the unique sequence level. If you wanted to go down the phylogenetic route, you could do the following:

dist.seqs(cutoff=0.15)  
cluster()  
make.shared(label=0.03)  
get.oturep()

dist.seqs() \<- using the fasta output of get.oturep  
clearcut()  
etc…And just replace your original names file with the output files from get.oturep().

The thing I want to check is whether there’s a problem using dist.seqs a second time around. I would assume that no cutoff needs to be specified because the sequences have effectively been filtered to that level of dissimilarity already? Is this correct?

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [November 6, 2012, 8:14pm UTC](https://forum.mothur.org/t/cluster-command-output/1114/4 "2012-11-06T20:14:32Z")

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Ugh. Yeah you could do this, but why? I think part of the intended beauty of the phylogenetic approach is that you don’t have to apply a cutoff.

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**Author:** ![dwaite](https://avatars.discourse-cdn.com/v4/letter/d/ecccb3/32.png) [@dwaite](https://forum.mothur.org/u/dwaite)\
**Post date:** [November 7, 2012, 1:58am UTC](https://forum.mothur.org/t/cluster-command-output/1114/5 "2012-11-07T01:58:11Z")

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I don’t know how valid these reasons are (hence the asking), but the reasons I’ve been thinking about it:

Firstly, just as a data reduction technique. The SOP is to dereplicate, removing identical sequences to reduce the processing requirements. This is really just reducing your data into unique OTUs, so using a lower similarity threshold (say, 97% similarity instead of 100%) is just an extension of this. That said, I realise that the output of get.oturep is not a consensus sequence.

Also, regardless of whether you want to to an OTU- or phylogeny-based analysis, the traditional ecological diversity measures are those used in the OTU approach and I think it’s important to keep these in the workflow. That said, if you end up calculating Chao1/Simpson/Shannon/whatever estimators at a level other than unique, you’re going to dissociate the results of these calculators from the data you’re running through a unifrac. Case by case, it might be interesting to see if the most abundant OTUs are all phylogenetically similar (eg. different strains of _E. coli_) or quite different, and the only ways I can see to do this are to look at their taxonomies (if they’re very different, and only for broad comparison), or to do the method I said above.

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**Author:** ![miguelangel](https://avatars.discourse-cdn.com/v4/letter/m/e8c25b/32.png) [@miguelangel](https://forum.mothur.org/u/miguelangel)\
**Post date:** [November 7, 2012, 10:36am UTC](https://forum.mothur.org/t/cluster-command-output/1114/6 "2012-11-07T10:36:14Z")

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Thank you very much. I’ve run get.oturep and it worked perfectly.