How to work with many .qual files in a single step ?


I have paired end 16S sequences from Miseq data. I am preparing qual files using Then I do make.contigs. At the step of Trim.seqs, I want to use command ‘‘mothur > trim.seqs(fasta=xyz.fasta, qfile=xyz.qual, qaverage=28)’’.

When I make qual files, I do that for forward and reverse sequences each seperately for each sample. As a result I have many qual files generated. Is this approach correct?
Then I do make.contigs and then go to trim.seqs.

My question is that how can I input so many qual files together at this (Trim.seqs) step together, so that I can do quality filter of all my data based on quality scores in a single step?

I am sorry if I asked very basic question.
Looking forward,

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