Remove.groups with low seqs count before sub.samples 454SOP

Commands in mothur
1

Normalization to the group with lowest sequence count is demonstrated as a must, however, if one of the samples has a low count (in my case 160 seqs), how can i remove those samples or groups.
here how i did it but not sure if it is the most efficient way:
i went back to files prior to OTU analysis i.e.
final.names
final.fasta
final.groups
final.taxonomy

and removed the unwanted groups:
remove.groups(fasta=final.fasta, name=final.names, group=final.groups, taxonomy=final.taxonomy, groups=G2-G3-G6-G7)


Removed 6281 sequences from your name file. Removed 2530 sequences from your fasta file. Removed 6281 sequences from your group file. Removed 2530 sequences from your taxonomy file.

Output File names:
final.pick.names
final.pick.fasta
final.pick.groups
final.pick.taxonomy


then i redid the dist.seqs, cluster, make.shared, and count.groups and finally finishing with sub.samples.

Is this the correct or best way, since re"cluster"ing takes lots of time.

many thanks

2

Hi there,

So you can do remove.groups or you can just put everything through cluster. Then you can rarefy or subsample everything to a given number of reads per sample and those with fewer reads than your threshold will automatically get tossed.

Pat

3

great thanks.