Questions with Mothur in Galax.EU
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3.2 years ago
  1. We think that like our sample are very lot sequences and OTU, Would it be better to upload fewer samples at once? meaning, we have 92 samples, we can try to upload 30, later others 30 and finally 32. However, Is there some command for later join all samples for getting OTU´s information?

  2. In the step "Cluster.split" we should put this parameters:

    Cluster.split tool with the following parameters
    “Split by” to Classification using fasta
    “fasta” to the fasta output from Remove.groups
    “taxonomy” to the taxonomy output from Remove.groups
    “name file or count table” to the count table output from Remove.groups
    “taxlevel” to 4
    “cutoff” to 0.03
    

The taxlevel = 4 correspond to the level of "Order". So, we thought that

  • taxlevel=2 = level phylum;
  • taxlevel=3 = level Class;
  • taxlevel=5 = Family;
  • taxlevel=6 = Genus;
  • taxlevel=7 = Species.

Then we ran the command Cluster.split using taxlevel=2, however, the result was a similar file, with 2 less species and less OTU than with taxlevel =4. So, we do not understand very well the use of taxlevel. Can you explain us, please?

Thank you very much

Lourdes

sequence mothur • 722 views
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