ipig(1) Integrating PSMs Into Genome browser visualizations




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.


<psm file>
-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