I have just begun to try ‘MiSeq_SOP’ with the example data that can be downloaded from its webpage and I have encountered a problem (well, maybe not a problem, just a doubt) with the first command that appears in the SOP: make.file.
I have tried to generate my own ‘stability.files’, although there is one coming with the data. I run the mothur.exe from the same folder where the ‘MiSeq_SOP’ data folder is, not from another one copied ‘into’ that folder. So I type on the prompt
make.file(inputdir=MiSeq_SOP, type=fastq, prefix=stability2)
And as a result I get a file named ‘stability2.files’, as it was expected.
However, when I look it in deep I see that I have a file where all the rows in the first column are identical (“MiSeq”) and all the .fastq files (both the R1 and the R2) have a name begining with ‘MISEQ_SOP’.
Therefore, when trying to run the second command in the SOP, ‘make.contigs’, I get a result (‘Group count’) telling me that all the sequences belong to a unique sample, named ‘MISEQ’.
How can I do to make the command ‘make.file’ identifies the samples as different, I mean, match up the R1 and R2 from the same sample and then identify each sample in the inputdir as different?
Thanks a lot