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- TPP:Developer Documentation (23931 bytes)
216: ...=Processing peptide data with the pipeline (using xinteract)====
217: ...o apply all or some parts of the pipeline. Type 'xinteract' with no arguments for usage instructions.
384: ====xinteract====
385: xinteract (generaloptions) (-Oprophetoptions) (-Xxpressopti...
459: ;xinteract *.xml - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
228: - Scroll to bottom and (Run XInteract) - Software:Out2XML (2805 bytes)
9: ...automatically, either throught the TPP GUI or the xinteract command.'' - TPP:Mascot and the TPP (957 bytes)
25: * Run xinteract as usual - TPP Tutorial v1 (43187 bytes)
283: ...inally under ‘Run Analysis’, click the ‘Run Xinteract’ button'''
295: '''xinteract -NraftTPP.pep.xml -Oi -X-m1.0-nC,8 -A-1C-mC8 *.xm...
422: xinteract -NraftTPP.xml -p0.05 -Oip -X-m1.0-nC,8 -A-1C-mC8 ... - Software:TIQAM (7374 bytes)
21: ...ile is generated by the [[Software:TPP|TPP]] when xinteract is run. - Expert search and TPP usage (12929 bytes)
41: echo “ -OdA -dDECOY_ -E<experiment_tag>” > xinteract.params
43: ...run on the search results based on whatever is in xinteract.params and the results, including Mayu and calctp...
58: ==== xinteract (TPP) parameters for X!Tandem searches ====
60: For a listing of all xinteract parameters, type xinteract | more.
62: Here is a sample xinteract.params file for an X!Tandem search using decoys o... - Terry's blog (18394 bytes)
76: * Establish this practice: always run xinteract (PeptideProphet) with -E (experiment_label) flag.... - Building Peptide Atlas (26978 bytes)
14: ...y; to avoid running iProphet you will need to run xinteract manually because scripts such as runtandemsearch ... - Alt NxST search strategy (1763 bytes)
42: # Create or copy over an appopriate xinteract command
43: ...regis/sbeams/archive/sbeams/conf/xinteract.cmd.ft xinteract.cmd
45: # Run xinteract
46: ./xinteract.cmd - TPP:4.2.0 Release Notes (4364 bytes)
76: **New iProphet tab, plus support within xinteract
77: **Added NOMNC option to xinteract - Processing glycopeptide data (6720 bytes)
60: # Run xinteract
107: # Run xinteract. - TPP Tutorial v2 (15736 bytes)
89: ...Pipeline'' section in ''Petunia'' to access the ''xinteract'' interface.
90: ''xinteract'' is a general utility that is able to launch
94: ...ptions set to their defaults, and click on '''Run XInteract''' at the bottom of the page to run ''PeptideProp...
123: ...Pipeline'' section in ''Petunia'' to access the ''xinteract'' interface again.
139: ...ptions set to their defaults, and click on '''Run XInteract''' at the bottom of the page to run ''ASAPRatio''... - TPP:4.3.0 Release Notes (13496 bytes)
251: * Adding Lys-C enzyme option to xinteract.
303: * xinteract: don't do pepxml indexing when running headless (... - Custom digest site (3924 bytes)
49: * Next, open '''src/Visualization/xinteract/xinteract.cxx''' for editing - Msconvert Capabilities (15313 bytes)
15: xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211605 (li...
75: xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211605 (li... - TPP:4.4.0 Release Notes (31941 bytes)
52: === xinteract ===
203: [xinteract] skip the iprophet stuff for LabKey purposes (cur...
302: [xinteract] when creating or running regression tests, ignor...
438: xinteract PHOSPHO model and enable option InteractParser -P...
495: === xinteract === - TPP:4.5.0 Release Notes (8358 bytes)
16: * xinteract - TPP:4.5.1 Release Notes (4270 bytes)
21: ...if all files in same dir (shorten command line) [xinteract only at the moment]
32: * Change xinteract to run RefreshParser before PeptideProphet - TPP:4.5.1 SVN Log (9734 bytes)
115: ...shorten shell command size); implemented this for xinteract, the biggest culprit.
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