I am just wondering about the options for matching. Particularly, the manual says:
"There are two flavors of matches that should be mentioned [...] The second definition is that a match is defined as the unique combination of the upstream portion of N hits, and the unique location of the downstream partner as defined by a particular geometric constraint. In this case, multiple groupings of hits that are enumerated can map to the same match. This second definition, in the code referred to as a "match_dspos1" since the down-stream (ds) position is defined by a single geometric constraint, reduces the number of matches that need to be considered for output considerably; this makes matching faster and avoids the problem of producing thousands of nearly-identical output files which frustrate post-processing."
But the manual doesn't seem to clearly indicate which options enable or disable match_dspos1.
Also, a question to veterans of matcher and enzdes - from your experience what are the best options to enable to speed up matching and minimize redundant or very similar results, while maintaining as many unique matches as possible? How many matches is considered reasonable for subsequent analysis with enzdes? What is the best grouper to use for subsequent enzdes?
Thank you for your advice!