Dear Mothur users,
I was wondering if it is possible to merge groups in a “.shared” file.
E.g. if I would like to generate a Venn diagram on basis of a “.shared” file that contains 6 groups I would get “Error: Too many groups chosen. You may use up to 4 groups with the venn command”… which makes perfectly sense of course.
However, if my shared file contains e.g. 3 groups of Winter sequences and 3 groups of Summer sequences, would it be possible to merge those groups in two “seasonal groups”? This would allow me to generate a Venn diagram (or tree, pca etc.) based on those seasonal groups.
Obviously I could merge fastas and start from scratch but I am always interested in short cuts.
Best,
Guus
Hi Guus,
I’m pretty sure that wouldn’t work. While the merge.files command would certainly create a new file combining the matrices from your *.shared files, the resulting file would just list one matrix after the other instead of merging them into a combined list of shared OTUs. As you suspected, you would have to merge the *.fasta files, reprocess them, and create a new *.shared file for your seasonal treatments. I’m not a mothur guru by any standard, but I imagine this has to do with how mothur bins OTUs with the cluster() command. If you run cluster() separately for “Summer” and “Winter”, mothur will bin the sequences into different OTUs for each season.