Cluster.seqs question

Commands in mothur
1

Hello

I have a little problem with the cluster.seqs command

I’m working on a pipeline and I have troubles with some datasets

Sometime, the distance I want is not created in the list output (I want 0.05 but the command didn’t calculate this distance)
I know that if a distance is the same than the next smallest distance, this distance will not be in the list file

My problem is that when I do the remove.rare command with the option label=0.05, since this label is not in my file, the command output name is not what my pipeline expected

I want to know if I take the list file and I manually add the line 0.05 by copying the next smallest distance, will it work or will it cause problems

Thanks in advance

2

A better option may be to take advantage of mothur’s “current” option. Mothur will keep track of the current list file for you. You could run:

remove.rare(list=yourListFile, nseqs=yourNseqs, label=0.05) - remove the rare sequences from 0.05 in your list file or last label before 0.05
nextCommand(list=current) - mothur will use the list file generated by remove.rare