Thanks kmitchell. I would like to use the procedure ( https://github.com/krmaas/bioinformatics/blob/master/mothur.fungal.batch ) you have outlined for ITS analysis.
Question #1 – A special case for skipping make.contigs?
Our lab used a primer set that would amplify ITS1, 5.8S, and ITS2 regions.
This expectation is based on the yeast genome.
It turns out the length of PCR amplicon is about 750 bp.
We are using MiSeq 300 x 2 (PE).
Based on the gene coordinates, we consider that Read1 would have most of ITS1, whereas Read2 would span ITS2 and some portion of 5.8S.
This means there shouldn’t be a place where Read1 and Read2 overlap.
Hence, is it reasonable to skip the make.contigs() step in this situation? Thank you.
Question #2 – If it is okay to skip make.contigs(), can I apply the above procedure, respectively, for Read1 ( ITS1 ) and Read2 ( ITS2 ), in our specific case? Thank you.