---
name: "ipig"
section: "1"
platform: "linux"
package: "ipig"
version: "0.0.r5-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ipig"
---

# ipig(1)

Integrating PSMs Into Genome browser visualizations

## 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