in one of my datasets a number of sequences is long enough to contain the reverse primer and adapter while others do not. Because of this I wasnÂ´t able to use the reverse primer in the “trim.flows” and “trim.seqs” commands of my workflow as it would scrap the majority of my sequences for failing to recognize the reverse primer. Using only the forward primer the output was fine but now a large number of my sequences still have the reverse primer and adapter sequence at their end. Is there a way in mothur to remove these sequences if present without scraping any of my (otherwise fine) 454 sequences?
Thank you in advance for your help & best wishes,