This is the command ipig that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use ipig online using onworks.net services
