I am trying to follow Mothur MiSeq sop. I want to remove primers from my sequences while running make.contigs. My oligos file looks like this:
primer GGAGGCAGCAGTRRGGAAT CCCCGTCAATTCMTTTGAGTTT
However make.contigs puts all my sequences in *.scrap.contigs.fasta.
How can I get around this problem?
Thanks in advance for helping me out.