I am new to posting here so apologies in advance if it’s a mess of a question!
Within the function below, the minsim parameter is not working and seems to be filtering wrong (?). Having it set to 90 removes all my sequences. I have tried changing this parameter to a decimal (minsim=0.90), as that is how the similarity to template sequence result appears in the align.report file, but still too many reads are disappearing as almost all of them are above 90% similarity to the template sequence (and this has not been an issue before). The similarity score from align.seqs is not in decimal form, but it is in screen.seqs - could this be part of the issue/a bug?
screen.seqs(fasta=x.trim.contigs.good.align, alignreport=x.trim.contigs.good.align.report, minsim=90, minscore=10, group=x.contigs.good.groups)
I am using Mothur with ITS2 sequences, and have not previously encountered this problem. Other than coding a workaround or removing the minsim parameter entirely, I’m not sure how to solve this.
Thank you in advance!