I would like to export OTU data. To be more precise I would like to export data, so I could see what OTU-s are
represented by how many sequences in which groups.
Is get.relabund the command for it or would I have to mess around with mothur files containing otu information myself?
To clarify there is this example for a table I would like to create. (I was not able to format it better in here, hope you understand)
(otutable) otu1 otu2 otu3
sample1 234 seqs 543 seqs 245 seqs
sample2 0 seqs 400 seqs 220 seqs
sample3 200 seqs 0 seqs 300 seqs
The mothur wiki on get.relabund was not totally clear for me. I will post an abridged piece from one of the examples there -
get.relabund(shared=abrecovery.fn.shared, label=0.03)
0.03 B 168 0.000000 0.000000 0.000000 0.000000 0.000000 0.011905 …
0.03 C 168 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 …
0.03 A 168 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 …
So do I understand it correctly - There are 168 of OTU-s alltogether. As we can see there are no sequences from OTU1 in groups B and A though there are some
in group C (0.013514 of total sequences in group, where total is 1)?
Are the columns following 168 for OTUs? How are they sorted (can I use them OTU1, OTU2 etc. from left to right and be sure It is consistent with OTU nameing in other mothur commands)?
Where will I see the total number of seqs. in groups. In case I would like to find out the exact number of seqs. by which this OTU is represented in this group instead of abundance/ratio. (Not so important. Most statistical programs would like to see abundance table anyway, but who knows - I might need it.)