Trim.seqs when the read is from the Forward or Reverse


I’m trimming about 160 000 reads (454 data). It’s a control data set and there are no barcodes. My sequence provider says we can get reads in both directions because the amplicons ligate to the adaptors in either direction. To trim, must I use trim.seqs with my fasta file and the forward primer and then repeat this step with the reverse primer (and flip the sequences) or is there a way to tell the program to trim either the forward primer or the reverse primer? One colleague suggested just putting two forward primers in my oligos file.

Thank you for any input and advice!

Best wishes,

Try the checkorient option…