The previous mothur version I was using did not have the oligos option, so I am hoping to get clarification on this. I have fastq files that have barcodes removed but presumably still have the 16S V4 primers attached. The program I use to demultiplex can trim primers but only based on primer length, so I opted out based on that seeming a little cruder than I’d like. I decided to take advantage of the oligos option in make.contigs but I’m confused on the right setup. First I made a .file with two columns:
Then my oligos file is formatted for pcr.seqs as such:
When I ran
make.contigs(file=oil_sed.file, oligos=oil_sed.oligos, processors=24)
I got the following error:
make.contigs requires paired barcodes and primers. You can set one end to NONE if you are using an index file.
Am I required to supply barcodes (unnecessary since mine have been removed)? If I don’t need barcodes, I am thinking I need to format a specific oligos file for make.contigs which looks like this:
primer GTGYCAGCMGCCGCGGTAA GGACTACNVGGGTWTCTAAT