SYNOPSISipig <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)
- 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