I created a stability file with three samples of interest, followed the MiSeq SOP, and got results! But alas, there’s some confusion.
How can I tell which OTU goes to which sample from the “stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.opti_mcc.0.03.cons.taxonomy” file?
Is there a certain command I can run?
I am a little confused about what exactly you are asking for, so ignore this if i’ve missed the mark.
The .shared file will tell you what OTUs are in what samples (and their abundance in each sample), the .taxonomy file tells you what each of your OTUs is classified as, but not what sample that OTU was in, that information is in the shared file. You can however combine all this information into one file with create.database to have a single file with abundance of OTUs in each sample along with their classifications (and if you want their representative sequences).
We have a bug in make.file that will be corrected in our next release. The bug effects the sample names generated by the make.file command. Can you check your stability.files file and make sure the names are unique?
Thanks for the responses! That answered my question.
I can check the data sometimes this weekend and will report back.