NAME

       ipig - Integrating PSMs Into Genome browser visualizations

SYNOPSIS

       ipig <psm file> |-g|-c|-cg [<config file>]

DESCRIPTION

       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