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

1

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

2

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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3

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

4

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