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  • Mothur Classify OTU Problems

    Hello,

    I keep coming across an issue at the classify OTU step.

    The label is set at 0.03 to determine a 97% similarity between OTUS.
    After I run the command mothur output says "Your file does not include the label 0.03. I will find the next smallest label 0.16"
    This set alls of my data to 84% similarity.

    Has anyone experienced this issue before?
    Do you know why the label would not work?
    Does it have to do with the SILVA file folder I have to use for the taxonomy?

    Any responses are helpful.
    Thanks!

    Ashlee
    Last edited by albreaks; 03-13-2017, 07:15 AM.

  • #2
    Without knowing anything about your samples or commands run, it's not possible to help. The mothur forum is pretty active, I suggest looking through that and potentially posting there if you can't find an answer.
    Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

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    • #3
      Ashlee,

      Can you post the command that specifies 0.03?

      I wonder if the 0.03 requires a unique processing step back a few more commands to appropriately set your data correctly for the 0.03 you mention to work?

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      • #4
        The command is as follows:
        classify.otu(list=rumenAB.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.unique_list.list, count=rumenAB.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, taxonomy=rumenAB.trim.contigs.good.unique.good.filter.unique.precluster.pick.rdp.wang.pick.taxonomy, label=0.03)

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        • #5
          go to the mothur forum and explain in more detail what your samples are, sequenced region, etc along with all commands

          Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

          Comment


          • #6
            Thank you for the help!

            Comment

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