New beginner ( how to start working by mothur)

I am really new in the mothur, I have some miseq data that I want to analysis them by mother, actually I have 6 samples ( 12 fastq files ), my question is how can I merge them ? I using computer in university lab that installed mothur. I need a toturial that very simple that step by step. I found several but they are not useful for me. thanks

I think MiSeq SOP from is very simple. First make stability.files for your six samples as explained in About the stability.files You need to download Silva v123 (Full length Sequences and taxonomy references) files from (.align file to be used as reference). Also you need to download 16S reference PDS files from to be used later inthe SOP. Then follow MiSeqSOP. Hope this helps.

thanks for your reply .
I used some of commands but none of them worked. for example i used set.dir but it says invalid command. I do not know what is the problem

Oh sorry I don’t know what that problem is. But what I do is I put all my files and reference files in one directory and run mothur. The output files will be in the same directory, which can be exported later on.

what do u mean by reference files? I made a stability files and put it and my fastq files in one folder and then run make.contigs by this commands

but it says there is a syntax error ? thanks for help

I think the reference files itsbinit meant are the silva taxonomy files you will need later. Regarding your ‘set.dir but it says invalid command’ problem, did you input your command properly? Like:


Yes, That’s right, reference file I mean are silva.nr_v123.align, and trainset14_032015.pds.fasta which you will need later in the process. I am too beginner in mothur and I strictly followed the MiSeq SOP to generate the output files. Like I said before I did not set input and output directory, all my input files, reference files and output files generated are in the same directory. Once I made the stability.files in that same directory, I called mothur from within the same directory and ran make.contigs(file=stability.files) It worked.