Hello,
My amplicon is 177bp, but the maximum length of sequences ranges from 150-301bp after I run make.contigs.
When running screen.seqs, is it important to very stringent (i.e. maxlength=177), or should a certain degree of flexibility be provided here?
Thank you,
Jo
Yeah i’d be a bit flexible. One thing you might try is to see what the length variation is in silva.bacteria.fasta (or whatever database) and then use that to guide your max sequence length.
Pat
Thank you for this, Pat! Much appreciated.
One final question…how should I go about checking the variation in length within the database? Is there a particular command to enable me to do this?
Jo
You could try running pcr.seqs with your primers against silva.bacteria.fasta or trainset9.fasta and then run the output through summary.seqs.
Pat