MiSeq SOP screen.seqs

I am running through the MiSeq SOP and have a question about the implementation of the screen.seqs command.

When removing sequences with ambiguous bases and anything longer than a certain bp threshold, there seems to be two approaches:

  1. mothur > screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, maxlength=275)
  2. mothur > screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, summary=stability.trim.contigs.summary, maxambig=0, maxlength=275)

In both cases it seems that you need to specify the maxambig and maxlength parameters. In the second case, is providing the two parameters (maxambig and maxlength) necessary even though I’ve already provided the summary file? If I’m creating a custom workflow batch file, how can I know those values in advance?

Chris D

The summary file case helps to speed things up since those values were already calculated in summary.seqs. If you don’t provide the file then screen.seqs has to do the calculations. You would never want anything but maxambig=0 and maxlength=275 is region dependent.