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?
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
taxlevel = 4 correspond to the level of "Order". So, we thought that
taxlevel=2= level phylum;
taxlevel=3= level Class;
Then we ran the command
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