Isn't the purpose of the base_name attribute in the pepXML to avoid the requirement of keeping the
basename of the files the same?
-Matt
On 8/3/2011 5:32 PM, David Shteynberg wrote:
I would suggest you run these in separate directories maintaining the
same basename of your spectrum files, this way iProphet will be able
to recognized multiple searches of the same spectra. Run xinteract on
each search combining all fractions from each search into a single
analysis at the PeptideProphet level. Something like:
cd sequest
xinteract Band*.pep.xml
cd xtandem
xinteract Band*.pep.xml
cd ../iprophet
InterProphetParser ../sequest/interact.pep.xml
../xtandem/interact.pep.xml interact.iprophet.pep.xml
Write back if you need further clarification.
-David
On Wed, Aug 3, 2011 at 3:06 PM, Kinfai Au<[email protected]> wrote:
Hi,
I have a data with 8 factions. I searched them in SEQUEST and X!tandem
respectively. The output files after PeptideProphet are:
Band1.sequest.pep.xml
Band2.sequest.pep.xml
Band3.sequest.pep.xml
Band4.sequest.pep.xml
Band5.sequest.pep.xml
Band6.sequest.pep.xml
Band7.sequest.pep.xml
Band8.sequest.pep.xml
Band1.xtandem.pep.xml
Band2.xtandem.pep.xml
Band3.xtandem.pep.xml
Band4.xtandem.pep.xml
Band5.xtandem.pep.xml
Band6.xtandem.pep.xml
Band7.xtandem.pep.xml
Band8.xtandem.pep.xml
How can I merge them in InterProphet? I asked this question in the
workshop. I work on Linux. Could you write me an example of the
command line that I should use?
Yours,
Kinfai
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