We use Mothur to do QC on non-demuxed highly-multiplexed amplicon sequencing data. We have over 700 primers, and make.contigs used to provide a group file split by sample and primer pair. That group file listed
sequence in column 1, and
sample_name.primer_pair_name in column 2.
This “feature” seemed to be an unintended side effect that just happened to let us do exactly what we wanted using Mothur.
We are using version 1.44.0, and this group file doesn’t seem be produced now. I’ve tried passing make.contigs my R1, R2, I1, and I2 files directly, and I’ve also tried using a 4-column
sample.paired.files file as shown in the Mothur manual. I’m also passing it an
oligos file with primer and barcode info as described in the manual.
I’m happy to provide any output that helps illustrate my question. I’m just wondering if it’s still possible to get the group file that groups by sample and primer pair?
EDIT: The last version this feature worked in was v1.43.0.