Provided by: ipig_0.0.r5-3_amd64
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