mothur

Cut off at "dist.seqs" and "cluster" steps for Genus level analysis

Hi community!!!

  • I want to compare the control and test samples at “Genus” level. Can anyone please tell me what cut off should I use at dist.seqs and cluster step?

Thanks and Regards,
DC7

For genus level data, you should follow the instructions in the MiSeq SOP for using phylotype data. There’s no meaningful distance threshold for species, genus, etc.

Pat

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Thanks a lot Dr Schloss.
I have seen in the SOP the phylotype(), make.shared(), and classify.otu() steps. And in forum, one person suggested to use filter.shared() step. So, I am using the following steps in order. Are the steps ok?

mothur > phylotype(taxonomy=stability.paired.trim.contigs.unique.good.filter.unique.precluster.pick.gg.wang.pick.taxonomy, count=stability.paired.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table)



mothur > make.shared(list=stability.paired.trim.contigs.unique.good.filter.unique.precluster.pick.gg.wang.pick.tx.list, count=stability.paired.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, label=1-2-3-4-5-6)


mothur > filter.shared(shared=stability.paired.trim.contigs.unique.good.filter.unique.precluster.pick.gg.wang.pick.tx.shared, label=2)



mothur > classify.otu(list=stability.paired.trim.contigs.unique.good.filter.unique.precluster.pick.gg.wang.pick.tx.list, count=stability.paired.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, taxonomy=stability.paired.trim.contigs.unique.good.filter.unique.precluster.pick.gg.wang.pick.taxonomy, label=2)

Thanks and regards,
DC7

You don’t want to use filter.shared. Either use label=1 in make.shared or in classify.otu and your downstream functions.

Pat

1 Like