Could I do subsequent analysis with Mothur after I have an OTU table already, and how?

Commands in mothur
1

Hi,
I’m quit new to mothur, and working on my recently back dataset. I got help from our bioinformatician and get the OTU table finally. I would like to use mothur to do some more analysis, like diversity calculations etc. Should I change my ready OTU table to some biom format, or shared format? I tried those two commands, but they didn’t work for my table. I’m thinking maybe it’s arrangement of the table is not right, it looks like below. Anyone knows what should I do? Thanks a lot in advance! :smiley:

Samples OTU-0 OTU-1 OTU-2 OTU-3 OTU-4 OTU-5 OTU-6 OTU-7
sample1 29269 1480 0 85 6 42 270 3
sample2 40828 465 1 35 0 106 124 13
sample3 5222 33180 1 2245 1 138 285 34

2

A shared file looks like so…

http://www.mothur.org/wiki/Shared_file

The main difference between this and yours is that you need the first column to be some made up label that is the same for all of the samples. You also need a column between your Samples and OTU column that is the number of columns that follows. This will be the same number for all of your sequences.

Pat

3

Thanks for your answer! I made the shared file now, but when I run the make.biom, it turned out having a problem with
Segmentation fault (core dumped), is this a memory problem?

4

Could you post a sample of your new shared file?