I am trying to use ANOSIM to compare two soil samples’ bacterial profiles. I currently follow the MiSeq protocol and I was hoping someone could give me pointers on when to run this command. I build a distance matrix (can be square or not), but I don’t know how to make a design file. I have tried making it using the file names I originally gave my sequences, but I always get an error message that says the files were not found.
My questions are:
- How do I make a proper design file?
- Do I need more than one file in each “group” of the design file.
A design file is basically just a ‘group of groups’ file. It looks the same as the groups file, but instead of clustering sequences into groups it clusters groups into bigger groups (or as I think of it, samples into treatment groups).
It’s just a tab-separated text file with your group names followed by treatment. E.g.
For your second question, if you're asking whether you need to have something like the above, rather than, say;
Then I would imagine the answer is yes, because ANOSIM is comparing your within- to between- group (treatment) variation so would require some replication to get a measure for the intra-treatment variation.