Hi Bernt, This was only an example. In my work I organise my searches in different directories. This is not the only way this tool can be run. What you suggest is an acceptable alternative.
-David On Sun, Jul 12, 2009 at 11:38 PM, Bernt<bern...@gmail.com> wrote: > > Hi David, > > With reference to the iProphet usage, as described in your post: > > InterProphetParser exp1/sequest/interact.pep.xml exp1/xtandem/ > interact.pep.xml exp1/mascot/interact.pep.xml exp2/sequest/ > interact.pep.xml > > Do the pepxml files for the different search results (i.e from mascot > and xtandem) have to be placed in separate folders to create that "/ > xtandem/interact.pep.xml" file string recognition? If the > interact.pep.xml files are named differently to indicate the different > searches performed, is it not sufficient? > > And do the pep.xml files for tandem and Mascot searches have to be > renamed with exactly the same extensions and filenames (i.e. > *.tandem.pep.xml -> *.pep.xml and *.dat.pep.xml -> *.pep.xml) for > PeptideProphet to add the -E expt label? > > > Bernt > > > On Jul 1, 2:39 am, David Shteynberg <dshteynb...@systemsbiology.org> > wrote: >> Hi Greg, >> >> TheiProphetpowerful tool that is very simple to run. Unless you are >> testing the performance of the various modelsiProphetapplies, there >> is not need to setiProphetparameters. The easiest way to run the >> tool is on a single analysis (one experiment, one search engine), >> this only requires enabling the xinteract -ip option which will >> runiProphetand ProteinProphet inIPROPHETmode in parallel to the >> standard analysis. >> >> A more complex analysis can be setup for combining multiple >> experiments and multiple search engines. The individual search engines >> and experiments must first be analyzed using xinteract (using option >> -E<experiment_label>) where the different searches of the same data >> get labeled with the same <experiment_label>. You can then runiPropheton >> the PeptideProphet results using the InterProphetParser >> tool. >> >> Running it on the commandline without any arguments produces following >> the usage statement: >> >> usage: InterProphetParser <file1.pep.xml> <file2.pep.xml>... <outfile> >> >> Where each of the input pep.xml files must come from a PeptideProphet >> analysis, and the spectra that were searched with different search >> engines have the same experiment_label spectrum_name combination. The >> outfile is a name of the pep.xml file whereiProphetwill write the >> results. For example: >> >> > InterProphetParser exp1/sequest/interact.pep.xml >> > exp1/xtandem/interact.pep.xml exp1/mascot/interact.pep.xml >> > exp2/sequest/interact.pep.xml exp2/xtandem/interact.pep.xml >> > exp2/mascot/interact.pep.xml interact.iproph.pep.xml >> >> To run ProteinProphet on theiProphetresults you can use the command >> >> > ProteinProphet interact.iproph.pep.xml interact.iproph.prot.xml >> >> -David >> >> On Tue, Jun 30, 2009 at 9:33 AM, Greg Bowersock<bowers...@gmail.com> wrote: >> >> > Just bumping this one up, since it looks like it got missed. >> >> > On Jun 10, 12:08 pm, "bowers...@gmail.com" <bowers...@gmail.com> >> > wrote: >> >> I was wondering if someone could post some more detail oniProphet. >> >> One thing that I would like to know is what all command line arguments >> >> it takes, maybe some sample command lines, as that is how I work with >> >> the TPP tools. I've gotten a little behind on some of the newer tools, >> >> but I thinkiProphetis something I've been looking for. >> >> >> Thanks, >> >> Greg > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
