I have Myseq paired end reads with barcodes at both ends (after merging fwd and rev) + primers, and I want to demultiplex at sample/barcode level trimming the barcodes and primers.
When I do the commands: trim.seqs and fastq.info it gives me an error: “cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting.”
the oligos file looks like this:
barcode NAACAAC NNAACAAC x1
barcode NNAACCGA NNNAACCGA x2
the command looks like this:
trim.seqs(fasta=my_Assembled_Read.fasta, oligos=My_Oligos_File.oligos, checkorient=T)
I don’t understand if the configuration of my oligos file is wrong or if it’s not possible to trim in one go paired barcodes and primers…
Thank you in advance for your help.