crux percolator

Usage:

crux percolator [options] <protein input> [--output-dir <psm folder>]

Description:

Percolator is a semi-supervised learning algorithm that dynamically learns to separate target from decoy PSMs. The algorithm is described in this article:

Lukas Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and Michael J. MacCoss. "Semi-supervised learning for peptide identification from shotgun proteomics datasets." Nature Methods. 4(11):923-925, 2007.

Crux now includes code from Percolator 1.05. The current version of Percolator can be downloaded here. External versions of Percolator can be applied to the output of the Crux tools, but won't be used by the crux percolator command.

Percolator requires as input two collections of PSMs, one set derived from matching observed spectra against real ("target") peptides, and a second derived from matching against "decoy" peptides. Crux generates these decoys on the fly. Percolator will also accept a second set of decoy PSMs and use one set in training and one in calculating q-values. Producing two sets of decoy PSMs is the search-for-matches default behavior.

NOTE: percolator requires that crux search-for-matches be run with the parameter top-match=1.

Input:

• <protein input > – The name of the file in fasta format or the directory containing the protein index from which to retrieve proteins and peptides.
• <psm folder> – [optional] A folder in which all the PSM result files are located. This is assumed to be crux-output, but it can be set by the user using the --output-dir option. The program looks for files ending in .csm, which are produced by crux search-for-matches. All such files in the given directory are analyzed jointly.

Output:

The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created:

• percolator.params.txt: a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.
• percolator.target.sqt: an SQT file containing the PSMs
• percolator.target.txt: a tab-delimited text file containing the PSMs. See txt file format for a list of the fields.
• percolator.log.txt: a log file containing a copy of all messages that were printed to stderr.

Options:

• --fileroot <string> – The fileroot string will be added as a prefix to all output file names. Default = none.
• --output-dir <filename> – The name of the directory where output files will be created. Default = crux-output.
• --overwrite <T|F> Replace existing files if true (T) or fail when trying to overwrite a file if false (F). Default = F.
• --parameter-file <filename> – A file containing command-line or additional parameters. See the parameter documentation page for details.
• --feature-file <string> – Optional file in which to write the features. Default = none.
• --verbosity <0-100> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.
• --version T – Print the version number and quit. Please note that you must include the 'T' after --version.

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