problems with trying to retrieve otu seqs

mothur bugs
1

hi guys;

so I did all the SOP stuff up until get.seqs for otus…when I do the get.seqs, the output has far fewer sequences than are actually present in the taxonomy file (using accnos and taxonomy). When I compare the taxonomy output:

  1. it doesn’t give me sequences instead it spits out a list of otus…which I guess makes sense, but the number of otus is not reflective of the taxonomy file, for example there are otus in the accnos that are clearly in the aligned and assigned tax file…

which brings me to my next question how exactly do you GET the taxonomic classifications from a list of shared otus? get.seqs doesn’t seem to give me any results…this is the resultant taxonomy file:

Otu00002 1
Otu00006 1
Otu00008 1
Otu00010 1
Otu00012 1
Otu00014 1
Otu00016 1
Otu00018 1
Otu00020 1
Otu00024 1
Otu00026 1

…it goes on with more of the same…what exactly am I doing wrong? this is what the taxonomy file references to in get.seqs is like (or at least the top few):
OTU Size Taxonomy
Otu00001 1 Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Otu00002 1 Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Otu00003 1 Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Otu00004 1 Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
Otu00005 1 Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);

2

the other alternative is to do get.otureps but the data set I want sequences from is as follows:

-I have 4 samples
-I want samples shared between 1-2-3 and absent in 4


In get otureps it doesn't seem like there's an otion to let you cherrypick like that.
3

It looks like you are giving it a *cons.taxonomy file, instead of a *.taxonomy file.

The *cons.taxonomy file is a consensus taxonomy for an OTU and looks like:

OTU Size Taxonomy
Otu0001 51464 k__Bacteria(100);p__Bacteroidetes(77);c__Bacteroidia(77);o__Bacteroidales(77);f__S24-7(67);g__(67);s__(67);
…

The *.taxonomy file contains the classifications for individual sequences, and looks like:

GQY1XT001DQU6D Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(83);unclassified;

The get.seqs command is designed to be used with a taxonomy file not a constaxonomy file.

Note: You might be looking for the get.otulabels command, http://www.mothur.org/wiki/Get.otulabels