Mayu
From SPCTools
| Revision as of 21:49, 16 July 2009 Tfarrah (Talk | contribs) ← Previous diff |
Revision as of 23:55, 18 July 2009 Tfarrah (Talk | contribs) Next diff → |
||
| Line 1: | Line 1: | ||
| - | Mayu, developed by Lukas Reiter at ETH, calculates decoy-based false discovery rates (FDRs) for proteomics experiments. FDR is calculated at the level of peptide-spectrum match (PSM), peptide identification, and protein identification. Protein length and possibly other attributes are taken into account. | + | Mayu, developed by Lukas Reiter at ETH, calculates decoy-based false discovery rates (FDRs) for proteomics experiments. FDR is calculated at the level of peptide-spectrum match (PSM), peptide identification, and protein identification. Protein length and possibly other attributes are taken into account. Mayu is written in Perl and accepts pepXML files, generated by either PeptideProphet or iProphet, as input. |
| - | Mayu is not yet shipped with the TPP as of July 2009. It has to be installed | + | Mayu is shipped with the TPP as of TPP v4.3.0, scheduled to be |
| - | separately. You can either download it from here: | + | released in late June 2009. |
| - | http://prottools.ethz.ch/muellelu/web/LukasReiter/Mayu/ | + | It can be found in trans_proteomic_pipeline/extern/Mayu. |
| - | ... or you can run it on our regis cluster at ISB. My understanding is | + | You can also download the Mayu software from here: |
| - | that everyone in Ruedi's group is entitled to an account on regis. | + | http://prottools.ethz.ch/muellelu/web/LukasReiter/Mayu/. |
| - | If you use regis, then Mayu is run automatically on iProphet results | + | It can be handy to run Mayu using the ISB-written wrapper |
| - | any time you use one of the scripts stored in /regis/sbeams/bin, such | + | MayuPepXML.csh, found in the same directory. Whereas Mayu.pl must be invoked from the directory |
| - | as /regis/sbeams/bin/tandem/runtandemsearch. Those scripts ultimately | + | containing the script, MayuPepXML.csh allows you to run Mayu |
| - | call another script, /regis/sbeams/bin/MayuPepXML.csh, to run Mayu. | + | on any pepXML file from within any directory, as follows: |
| - | MayuPepXML.csh can be run on its own on either a PeptideProphet or an | + | |
| - | iProphet file. Mayu processes PSMs (peptide-spectrum matches) and thus | + | |
| - | it does not make sense to run Mayu on ProteinProphet output. | + | |
| - | All of this assumes that you are familiar running the TPP from the | + | MayuPepXML.csh interact-prob.pep.xml |
| - | unix/linux command line. Mayu is not yet accessible via Petunia. | + | |
| + | Or, | ||
| + | |||
| + | MayuPepXML.csh /regis/sbeams/archive/youngah/HsUrine/HsNormFemUrine_163A/SPC_HsNIST2.0/interact-ipro.pep.xml | ||
| + | |||
| + | Output will be copied into the same directory as the input pepXML file. | ||
| + | |||
| + | Of course, if the directory containing the script is not in your $PATH (enter "echo $PATH" to find out), you will have to enter the entire pathname of the script, as in this example (your pathname will be different): | ||
| + | |||
| + | /regis/sbeams/bin/Mayu/Mayu.pl interact-prob.pep.xml | ||
| + | |||
| + | MayuPepXML.csh uses a basic parameter set when calling Mayu. | ||
| + | You can change the parameters by copying and editing the script. | ||
| + | |||
| + | Mayu is not yet available via Petunia. It must be run from the | ||
| + | Unix/Linux command line. | ||
Revision as of 23:55, 18 July 2009
Mayu, developed by Lukas Reiter at ETH, calculates decoy-based false discovery rates (FDRs) for proteomics experiments. FDR is calculated at the level of peptide-spectrum match (PSM), peptide identification, and protein identification. Protein length and possibly other attributes are taken into account. Mayu is written in Perl and accepts pepXML files, generated by either PeptideProphet or iProphet, as input.
Mayu is shipped with the TPP as of TPP v4.3.0, scheduled to be released in late June 2009. It can be found in trans_proteomic_pipeline/extern/Mayu. You can also download the Mayu software from here: http://prottools.ethz.ch/muellelu/web/LukasReiter/Mayu/.
It can be handy to run Mayu using the ISB-written wrapper MayuPepXML.csh, found in the same directory. Whereas Mayu.pl must be invoked from the directory containing the script, MayuPepXML.csh allows you to run Mayu on any pepXML file from within any directory, as follows:
MayuPepXML.csh interact-prob.pep.xml
Or,
MayuPepXML.csh /regis/sbeams/archive/youngah/HsUrine/HsNormFemUrine_163A/SPC_HsNIST2.0/interact-ipro.pep.xml
Output will be copied into the same directory as the input pepXML file.
Of course, if the directory containing the script is not in your $PATH (enter "echo $PATH" to find out), you will have to enter the entire pathname of the script, as in this example (your pathname will be different):
/regis/sbeams/bin/Mayu/Mayu.pl interact-prob.pep.xml
MayuPepXML.csh uses a basic parameter set when calling Mayu. You can change the parameters by copying and editing the script.
Mayu is not yet available via Petunia. It must be run from the Unix/Linux command line.
