Mock community in Mothur

I’m very confused how to include MOCK community sequences among my samples sequences in the “make.file” command in MOTHUR MiSeq SOP.
I’ve downloaded the Mock community used in HMP through BEI resources. but it’s just a single file and the rest of my samples are R1 and R2 fastq files.
When I run the “make.file” command which is “mothur > make.file(inputdir=., type=fastq” it generate 2 different files:
fileList.single.file: which contains the mock community files only
fileList.paired.file: which contains all my samples

Thank you.

Hi - the file you download would be used in the seq.error command. You need to generate sequence data for the mock community you are sequencing. Note that if you aren’t sequencing a mock community in parallel with your other samples, then you can’t analyze mock community data. You should have two files come off the sequencer for your mock community.


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