read.otu()

Commands in mothur
1

Hello
I use the command read.otu(), use the options: list and group. However, there is an error which says that :
Your group file contains 100000 sequences and list file contains 1434 sequences. Please correct.
For a list of names that are in your group file and not in your list file, please refer to unique.phylip.fn.missing.name.
I do have generated a missing.name file. So why I cannot read otu?

My command line is as follows:
read.otu(list=sogin.unique.phylip.fn.list, group=sogin.groups)

Thank you.

2

The read.otu command requires your list and group files to match. What you want to do is use the .missing.name file with the remove.seqs command to get a .pick.groups file that will match your unique list file. The command would look like:

remove.seqs(accnos=sogin.unique.phylip.fn.missing.names, group=sogin.groups)

then run the read.otu:

read.otu(list=sogin.unique.phylip.fn.list, group=sogin.pick.groups)

Hope this helps,
Sarah

3

Thanks it works.

However, I think use the pick.group may lose the abundance information. For example, I might not get the rarefaction of the entire community when I read.otu(list=sogin.unique.phylip.fn.list, group=sogin.pick.groups) rarefaction.shared(), for these are unique sequences rather than abundant sequences.

Would you please give me some advices?