xenial (1) ipig.1.gz

Provided by: ipig_0.0.r5-2build1_amd64 bug

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