I am new to MOTHUR and have just received a sequences from a MiSeq paired end run. The sequences had already been demultiplexed and had the barcode primers removed. However, the sequencing primers were not removed and I was given a file with the primers (515f and 806r) to the remove them. I am not sure how to do this.
I have tried using trim.seqs before and after make.contigs. When I use trim.seqs with my oligos file after make.contigs, I end up losing all of my sequences after the the filter.seqs step. When I use make.contigs followed by trim.seqs with my oligos file, Iater get a mismatch error after the unique.seqs step. I have also tried going from the make.contigs step through to the count.seqs step and then trimming the oligos but this causes MOTHUR to crash wen asked for a summary.
I’m not sure what is going on here, but any help would be greatly appreciated!