How to compare OTU lists

Commands in mothur
1

Hi there- I’ve used other software (usearch) to generate OTUs (clusters) of sequences from three of my samples- I would like to compare these OTUs now, and I’m not sure how I can do that. The goal is to make a cluster tree or heat map or some such output that lets me visualize the data, and also if possible use a test to see if they are indeed different in composition from one another. Can I take this data (fasta files of my OTU representative sequences), import it into mothur, and use some of the hypothesis testing or library comparison commands? Is there a way to export a table that lists sequences found among my samples and which ones are common to which samples, so I can generate a heat map? Can I use mothur for any amplicon, so long as they can be aligned? Can a kind person suggest which commands would be most appropriate to use? I’m not much of a bioinformatician and I’m trying to learn, so advice would be appreciated.

EDIT: OK, I see some of my questions have been answered by the wiki (oops) - but I still am hoping I can use my Usearch-generated OTU data and import it into mothur for sample comparison purposes. I am also hoping I can parse the names of the Usearch OTUs (which contain abundance information) so that can be used as well. Is this possible?

Liz

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Why not cluster them all together in USearch and then create your own shared file?

3

I’m hoping to use some of the hypothesis testing algorithms in mothur as well.

Is the read.dist command obsolete? I found a possible solution in some of the examples, but it requires use of this command and I get an error message that it’s an invalid command.

EDIT: OK, I seem to have figured it out now- but someone might want to go and add notes to the analysis examples that use the read.dist command. Thanks for writing this program, it’s doing a lot of things I can’t find ways to do otherwise!