How to trim the 454 data without barcodes

Commands in mothur
1

Dear all,

How can I trim the 454 data without barcodes?
Because all the barcode and key were removed by the sequence company, I just have files started with targeted primers. I tried to trim with a oligo file excluding bardcodes using trim.flows but all the sequences were scapted.

Best!

2

I would strongly encourage you to get the exact barcodes from the company and your sff files. They should be willing to provide this for you.