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