Hi Matt, Is it possible to turn off the decoy altogether in the search when there are decoy in the database? I tried a search with DecoyPrefix = "". Would that have the desired effect?
Thanks, -David On Fri, Mar 11, 2011 at 6:52 AM, Matthew Chambers <[email protected]> wrote: > 1. Yes. Set the DecoyPrefix parameter to whatever your existing decoys use. > 2. Interesting question, since ProteinProspector's new pepXML export is not > really flexible about how the decoys are indicated (it's always with a short > '-' prefix and the decoy protein accessions are always trimmed so that > "sp|P00001|BLAHBLAH" becomes "P00001"). > > -Matt > > > On 3/11/2011 6:15 AM, Ben Collins wrote: >> >> Hi, >> >> I'm trying to use myrimatch as one of a number of search engines to >> combine later with iprophet. It seems that later versions of myrimatch >> are doing on the fly decoy database generation, because I tried to >> search a database that already had decoys appended and ended up >> doubling up on the decoys. So my questions are: >> >> 1. Is it possible to switch of the on-the-fly decoy database >> generation in myrimatch so I can use a single database with decoys >> already appended for all search engines? >> >> 2. If its not possible to change the myrimatch decoy behaviour, will >> iprophet tolerate results from different search engines using non- >> identical databases? >> >> Many thanks for any advice, >> Ben >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
