.
Since you're using linux, build XPressPeptideParser from either the
trunk or branch4-5 code.
On Thu, Oct 20, 2011 at 2:04 PM, Ping yanpp...@gmail.com wrote:
Hi,
I installed tpp 4.5 on a Ubuntu 10.04 system. While I run
XPressPeptideParser on either XTandem/OMSSA serach result pep.xml
No I tired to on ubuntu 10.4 using installer_linux
The error message I got is after I run
sh ./install-prerequisites-ubuntu-9_04.sh
cd ../src/
make
Thanks,
Ping
On Oct 3, 4:34 pm, Joseph Slagel joseph.sla...@systemsbiology.org
wrote:
Are you trying to install using the window's installer
= fread(buffer,1,200,f);
saxmzxmlhandler.cpp:size_t temp= fread(buffer,1,200,f);
Thanks,
Ping
On Oct 4, 11:37 am, Ping yanpp...@gmail.com wrote:
No I tired to on ubuntu 10.4 using installer_linux
The error message I got is after I run
sh ./install-prerequisites-ubuntu-9_04.sh
cd
/mzParser/mzParser.h:3617: error: ‘uint32_t’ has not been
declared
Parsers/mzParser/mzParser.h:3618: error: ‘uint64_t’ does not name a
type
Did I do something wrong?
Thanks,
Ping
On Sep 21, 4:50 pm, Joseph Slagel joseph.sla...@systemsbiology.org
wrote:
Announcing the availability of Trans
Thanks Jimmy!
Is there any sequest.params sample with modifications I can get?
Thanks again!
Ping
On Mar 3, 5:16 pm, Jimmy Eng jke...@gmail.com wrote:
unless there's a way to convert .msf to pep.xml, and I'm not aware of
any tool that does this, you'll have to go the .out route.
On Mar 3
/sequest_params.php
What we really need is someone to contribute a .msf to pep.xml converter!
On Thu, Mar 4, 2010 at 3:49 PM, Ping yanpp...@gmail.com wrote:
Thanks Jimmy!
Is there any sequest.params sample with modifications I can get?
Thanks again!
Ping
On Mar 3, 5:16 pm, Jimmy
://proteomicsresource.washington.edu/sequest_params.php
What we really need is someone to contribute a .msf to pep.xml converter!
On Thu, Mar 4, 2010 at 3:49 PM, Ping yanpp...@gmail.com wrote:
Thanks Jimmy!
Is there any sequest.params sample with modifications I can get?
Thanks again!
Ping
Hi All,
The output of the Proteome Discover is *.msf. Is there an easy way to
compute peptide prophet from it? Or I have to run sequest.exe to get
*.out to do so?
Thanks!
Ping
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Hi All,
Has anyone build OMSSA under Ubuntu 64 bit? I got it successfully
complied along with NCBI tool kit, but it got very slow now. I noticed
that it only use one processor instead of original 8 processors to
run the omssacl.
Does anyone have any suggestion on this?
Thanks!
Ping
();
That is where I got the NAN error at the first point.
Thanks,
Ping
On Jul 14, 8:46 am, GATTACA dfer...@umich.edu wrote:
Ping,
Could you post what changes you made to the
NonParametricDistribution.cxx to fix the NAN error?
Thanks.
On Jul 9, 1:21 pm, Ping yanpp...@gmail.com wrote:
Jimmy
Hi,
I got a list of the search results which used different search
parameters, I already run InteractParser and PeptideProphetParser on
each of them. Is there an easy way to merge individual pep.xml into
one pep.xml file and with the hits ranked by peptide prophet?
Thanks,
Ping
suggested, I do
not need to replace the value in the protein with the first word
from the protein_descr in each search_hit entry.
Thanks again,
Ping
On Jul 6, 1:55 pm, Jimmy Eng j...@systemsbiology.org wrote:
Has anyone been able to feed OMSSA native pepXML output (using -op
option) through
to fix?
Thanks!
Ping
On Jul 2, 4:44 pm, Jimmy Eng j...@systemsbiology.org wrote:
Ping,
I just downloaded OMSSA 2.1.4 and tried the direct pep.xml export
myself. I do see a problem with the resulting pep.xml file that the
-op option generates that's causing the problem you're seeing
else I need to fix?
Thanks!
Ping
Here is the example of the result after I replace protein/
protein_descr
for not decoy string, it looks like this:
search_hit hit_rank=1 peptide=YPSRPLPFGLGFVPPYGPGR
peptide_prev_aa=R peptide_next_aa=I protein=gi|73975149|ref|
XP_862242.1| num_tot_proteins
: NCBI-BlastDL::Blast-def-line.title
Ping
On Jul 3, 3:46 am, Jake W jrwba...@gmail.com wrote:
One solution to this is to use the indexing option (-o T) in
formatdb when formatting your BLAST database for OMSSA searching. In
my experience, that will result in OMSSA writing the first word
Jimmy,
Thanks a lot for your explanation. I am going to write a script to fix
the pep.xml file and see how it goes.
Ping
On Jul 2, 4:44 pm, Jimmy Eng j...@systemsbiology.org wrote:
Ping,
I just downloadedOMSSA2.1.4 and tried the direct pep.xml export
myself. I do see a problem
alert the
developer !!!
I will try Jimmy's suggestion and see how it goes.
Thanks again!
Ping
On Jul 2, 7:15 pm, David Shteynberg dshteynb...@systemsbiology.org
wrote:
If you are running the tpp on the commandline you can correct this
problem in theomssaoutput by running the steps of xinteract
Is this something else and suppose to be a new post?
YP
On Jun 30, 11:08 am, Zhi Sun z...@systemsbiology.org wrote:
Hi all,
I just checked in two programs, and did not put the log message.
I will give a short description here:
createChargeFile.pl: this program reads the ms2 file
is searched under X!tandem. The result
I used is from TPP.
Thanks again!
Ping
On Apr 15, 3:42 pm, Luis Mendoza lmend...@systemsbiology.org wrote:
Hi Ping,
By the same results, do you mean that all of the program output is
identical? (e.g. the number of spectra used, etc) Or just that you also get
Luis,
Thanks a lot!
I just realize that the xml file from TPP output is already run
through PeptideProphet with 0.05 cutoff.
I will try to rerun the xtandem along to see how it works.
Best,
Ping
On Apr 16, 11:52 am, Luis Mendoza lmend...@systemsbiology.org wrote:
Hello Ping,
Yes, please
searched the post in the group, and used -p0 option, but still I got
the same results. Does that mean my original mzXML has too little low
quality spectral data?
Thanks again,
Ping
On Apr 15, 11:44 am, Luis Mendoza lmend...@systemsbiology.org wrote:
Hello Ping,
Qualscore uses a pepXML file
search for the same topic in the
group. Someone said it might because of the mzXML files?
Thanks again!
Ping
On Apr 15, 11:44 am, Luis Mendoza lmend...@systemsbiology.org wrote:
Hello Ping,
Qualscore uses a pepXML file with *all* PeptideProphet probabilities (i.e.
P=0.0). As such, you
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