QDD v3.1 users: Pipe1 settings?

[kpcoats]

I'm curious if any of you are using QDD v3.1 to mine for microsatellites, specifically from Ion Torrent assembled data? We have a pile of contigs assembled from a de novo sequencing of a fungus genome for the sole purpose of designing microsatellite markers and are having trouble (getting no or almost no primers from the QDD pipeline).

One of the aspects I'm looking into is the settings for Pipe 1. Do you change the defaults for Flanking Region Length (default= 200) or Sequence Length Limit (default= 80)? If so to what and on what do you base those changes?

[westerman]

Not for Ion Torrent data. For assembled Illumina data I've tried QDD a couple of times. Never changed the defaults though. It is pretty much a 'black box' to me.