make.shared, fasta file and the most abudant OTUs

Commands in mothur
1

Dear All,

I am trying to retrieve (from my fasta file) the OTUs that have more than 1000 sequences . This information is available in the make.shared output file

label Group numOtus Otu000001 Otu000002 Otu000003 Otu000004 Otu000005 Otu000006 Otu000007 Otu000008 Otu000010 Otu000011
0.03 night 94 2738 2459 1419 1354 882 746 1270 1184 1401 1157

however I am not able to use it to retrieve those sequences from the fasta file.

Many Thanks
Daniele

2

I think these commands will help: http://www.mothur.org/wiki/Filter.shared, http://www.mothur.org/wiki/List.otulabels, http://www.mothur.org/wiki/Get.otulabels, http://www.mothur.org/wiki/List.seqs, http://www.mothur.org/wiki/Get.seqs


make.shared(list=yourListFile, group=yourGroup) - create your shared file filter.shared(shared=current, mintotal=1000, makerare=F) - remove all OTUs with abundance less than 1000 list.otulabels(shared=current) - list otus with abundance >= 1000 get.otulabels(list=current) - select those OTUs from the list file list.seqs(list=current) - list sequences in abundant OTUs get.seqs(fasta=yourFastaFIle) - select sequences from fasta file in abundant OTUs
3

Many thanks for your help,

Just another question.
I was wondering if it would be possible to retrieve the OTUs that have sequence abundance comprised between 100 and 1000 sequences.

Thanks Again.

Daniele