mothur

Define Group in Stability File

Often times I’ll be working with data where my collaborator had, say, 100 samples, so we end up with 200 fastq files (forward and reverse). These samples don’t always correspond to groups, however, since we may be working with patient data, and sample multiple spots per patient. So, often we need to group the 100 samples into, say, 10 groups. It would be really awesome if, while I am defining my stability.file, I could also define the group that the sample goes in:

Sample1 sample1read1 sample1read2 GROUP1
Sample2 sample2read1 sample2read2 GROUP2
Sample3 sample3read1 sample3read2 GROUP1

etc. etc. etc.

We do have a merge.shared command that is intended for this purpose. It allows you to merge samples into bigger groups.

Pat

I can’t find this ‘merge.shared’ command on Category:Commands.
Is it still available in any other name?

Sorry… merge.groups

https://mothur.org/wiki/Merge.groups