mothur

Combining .shared files

Dear Mothur users

I hope everyone had a great week. I’m posting a query that has been posted before, but I couldn’t find a clear solution to this issue. I finished my workflow for another ITS dataset and got a .shared file at the end which looks like what I would expect from this system. However, when matching the otu data with my metadata, I realized that not all the samples downloaded into my folder from Basespace. More specifically, I was missing three samples (out of 300). I wasn’t aware of the fact that I had to run pre.cluster on all my samples together, so I just ran these three samples separately on my workflow and got a separate .shared file. I just realized that you can’t simply combine the two .shared excel files. As far as I understand, I need to merge the two fasta files and group files (latest version before pre.cluster) and then run pre.cluster on the combined files. I do not know how to merge these two group files. If there is an easy way to address this issue that someone is aware of, I would dearly appreciate your help.

Best
Nicolas

Why can’t you just use the merge.files command this way:
merge.files(input=fileA-fileB-fileC, output=fileABC) https://mothur.org/wiki/merge.files/
Do it for your fasta and then do again for your group and then run pre.cluster again using the merged fasta and merged group file.
I would recommend inputting the fasta files in the same order as you do the group files, when running the merge.files commands. I don’t know if it makes a difference, but since it’s a simple concatenation of files, I always input matching files, in the same order

It would probably be easiest to start from the beginning with all of the data.

Pat