I am not provided with an oligos file from our sequencer. I want to introduce oligos file to mothur when I am using trim.seqs command, but since I have my oligos in text file format can’t use it in the command. How can I produce an oligos file?
You have to the barcode and primer sequences from the sequencing facility. Once you have those, then you can make a text file that will be your oligos file (http://www.mothur.org/wiki/Trim.flows#oligos).
This tutorial will be helpful for you. It shows the basic format of a oligos file you could follow