I’m having an issue with the trim.seqs command. I have roughly 1400 Sanger sequences of 16S DNA. My goal is to remove the plasmid DNA remnants from each end of my 16S genes. I created an oligos file with the forward sequencing primer (near the EcoR I site of the plasmid) but did not include a reverse primer. I also did not include any barcodes or sequence identifiers. When I ran the command every sequence was placed in the scrap file but I found hundreds of sequences that had the correct forward primer. My oligos file, very simple, looks like this… (tab delimited)
command was this:
Do I need more in the oligos file to make this command run correctly? Should I be using a different command to trim my sequences?