ipig1

Usage

Overview

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/).

iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers.

Options

<psm file>

indicates the file with the peptide spectrum matches (mzid/txt)

-g, -gui

starts the graphical user interface of iPiG

-c, -control

starts the gene control, necessary files have to be indicated in the configuration file

-cg, -controlgui

starts the graphical user interface of the gene control

-d, -downloader

starts the download gui

<config file>

a different configuration file can be indicated (otherwise ipig.conf is loaded by default)

additional requirements:

using a non-gui mode, a config file (ipig.conf by default) has to contain several additional parameters, e.g. indicating the reference genome etc.

in a gui mode (-g and -cg), additional parameters can be indicated two ways, within the interface or with a config file as well.

have a look into readme.txt and ipig.conf for examples and more details about the additional parameters