I’m working with reads from Illumina Miseq.
The length of theoretical amplicon is about 400bp so we perform overlapping PE 2x250 .
I used make.contigs command only with stability file.
mothur > make.contigs(file=stability.files, processors=3)
It worked and I obtained stability.trim.contigs.fasta and I also checked contigs report file, but my worry is that primers and barcode could be probably inside the reads yet,
because I didn’t give to mothur information to trim them. It is true ?
Thanks in advance