Command Line

Running iPiG

To run iPiG from the command line, indicate the file containing the peptide spectrum matches (mzid) and a configuration file.

• Use "ipig your_psms.mzid" to run it with the default configuration file (ipig.conf) or
• Use "ipig your_psms.mzid your-config.conf" to indicate a different configuration file.

The configuration file has to contain several parameters, including the paths to necessary files, such as gene annotations or id-mapping files. Descriptions of the file types and formats as well as examples are given here: [Input Formats]. Further parameters are described in the sample configuration file "ipig.conf" provided with the tool.

iPiG will report the results in three different file types, BED, GFF3 and a text file similar to the alternative peptide spectrum matches input format described at [Input Formats] but extended by the mapping information (e.g. the determined locations). In addition, unmapped peptides are reported in a text file as well.
For details about the BED format visit http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
Details about the GFF3 format are available at http://www.sequenceontology.org/gff3.shtml

If you prefer using a graphical user interfaces (GUIs) have a look at [iPiG GUI].

Running GeneControl

In general, it is recommended to run GeneControl once for the gene annotations of each organism used. All files have to be indicated in a configuration file.

• Use "ipig -genecontrol" to execute the gene control with the default configuration file (gc.conf) or.
• Use "ipig -genecontrol your-config.conf" to indicate a different configuration file.

Descriptions of the required files and parameters are also given at [Input Formats] and in the sample configuration file "gc.conf".

GeneControl mainly creates 3 output files, named by the input gene annotation file extended by "_good.txt", "_bad.txt" and "_control.log". The "good" file contains gene annotations suitable for the mapping while rejected annotations end up in the "bad" file. The "log" file gives some hints about each rejected gene.

An example use of the GeneControl GUI is given at [GeneControl GUI].

Please note, after using GeneControl it is required to use the new gene annotation file ending with "_good.txt" instead of the original file for the mapping. Thus, you might have to change the entry in the iPiG configuration file.

Additionally, due to minor corrections of some annotations, the resulting filter set of gene annotations is not suitable for other usage than the iPig mapping, not even for GeneControl itself.