Under what commands can the design header file be incorporated?
Also, I have tried creating a design file using group names, but this has failed to work when incorporated in to the analysis, as the program is looking for the design file with the sequence names. How should the design file be formatted to include group names?
I’m not sure what you mean - are there specific commands where you’re having problems? Also, can you post an example of your design file that’s having problems and the error messages you’re getting?
There is a description on the wiki for a “Design Header File”, http://www.mothur.org/wiki/Design_header_file
It looks like this (from the example included on the page):
group treatment age sex
F003D000 F003Early old M
F003D002 F003Early old F
F003D004 F003Early old M
F003D006 F003Early young F
F003D008 F003Middle young F
F003D142 F003Middle other M
F003D144 F003Late other M
F003D146 F003Late middle F
F003D148 F003Late middle M
F003D150 F003Late middle M
It would be useful for some of the commands where a design file is required or an option (for example MetaStats), but I have not found any instance where it can be used.
Regarding my other comment about having difficulty with getting the design file to work, That was an error on my part. :o I was using the wrong input, and was able to figure it out. :oops:
The design file with headers can only be used with the make.lefse command.