get.microbiome which is which?

Commands in mothur
1

Hi, i ran get.microbiome and it sounds useful but i am having trouble understanding the output file. I have 28 samples and the left column states my samples from 1 to 28 . However, i can’t figure which group is samples 1? my groups are numbered G1 to G28. Anyhelp would be great .

O.

2

You mean get.coremicrobiome?

The first column indicates the number of samples that the OTUs are found in. From the wiki page:

The entries in the table represents the fraction of OTUs in a study that have a relative abundance at or above %X in at least %Y samples. X goes from 0 to 100, Y from 1 to the number of samples in your dataset. From the above file we can see that 0.615385 (roughly 62%) of the OTUs have a relative abundance at or above 0.01 in at least one sample, but only 0.230769 (roughly 23%) have a relative abundance at or above 0.01 in all the samples.

3

thanks Pat, the first column indicates the numbers of the samples but can these samples be defined i.e. when it says 5, 6, etc samples , can we determine those samples?

thanks

O.

4

That’s in the shared file. This command aggregates the data to see the % of OTUs that show up in N OTUs X% of the time.