chop cmd - define thresholds individually by ambiguities?

I’m fine with a cutoff of defined length at the front of the sequence read, but is there any way to have the end defined by the first ambiguous base? Some of my sequences are of better quality than others, therefore longer. I’d rather not lose information by chopping sequences at a distance defined by my worst quality read… is there already a way to do this that I missed?

Great project btw, and thanks for providing such amazing support for your software.

MrA,

I keep forgetting about this, but I think you can do it with the current version of mothur. Could you try setting qtrim=1 in screenseqs? something like…

screen.seqs(fasta=file.fasta, qfile=file.qual, oligos=file.oligos, qtrim=1)