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.
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
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.