Bjorn et al.,
Just like you I'm not familiar with the qualscore tool.
I was hoping to get some information from the spctools discussion list as to
what input files are necessary to run the qualscore tool.
The small documentation file mentions that one needs an interact.xml file as
input (see below)
The usage file clearly mentions that one needs an interact.xml file as input to
the qualscore tool, but apparently it also needs an underlaying mzXML file
holding the fragmentation spectra (see previous posting).
Since I'm converting my mascot .dat file to a .pep.xml file, I also end up with
a zipped file containing all underlaying peptide fragmentation spectra .tgz
instead of an mzXML file. I believe that is the reason why the software is not
running properly. Digging into the code is of course an option, but I was
hoping the get some useful feedback from this discussion list.
Regards,
Gerben
QualScore version 1.0_2 Copyright (C) 2006
Institute for Systems Biology, Seattle WA
QualScore is free software and comes with absolutely no warranty.
Usage: java -jar qualscore.jar <options> <interact-data file>
Input is interact-data.htm or interact.xml.
Output will consist of a set of .dta files determined to be high
quality unassigned.
By default the .dta files are written to a directory,
but they may also be listed to a file.
Options:
-c -c <number> Use Qualscore 'cutoff' instead of the default
Qualscore of 1.0 to determine which spectra are good qualit
y.
-p -p <number> Consider identifications with PeptideProphet
probability below <number> to be 'unassigned' (default is 0
.1).
-o -o <path> Tool output written to given path.
-l List spectra and quality scores to a file, rather than
writing to directory.
-lp List spectra, PeptideProphet probability, and quality score
to a file.
-a Used with -l (or -lp) to list all quality scores.
But while trying this I bumped into the an error stating that
On Oct 2, 2010, at 12:42 , Bjorn wrote:
> Gerben,
> I have no experience, but would like to use the tool (like you I
> suppose...).
> Is there any documentation on what file has to be where for qualscore
> to work?
> Thank you.
> Bjorn
>
> --
> 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.
