ipig - Integrating PSMs Into Genome browser visualizations
ipig <psm file> |-g|-c|-cg [<config
file>]
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>
- 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