ipig - 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.

       ipig - Integrating PSMs Into Genome browser visualizations

<psmfile>
              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

ipig 2012-06-19                                   February 2014                                          IPIG(1)

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