LaneRuler Documentation
LaneRuler - automated lane tracking software for electrophoresis gels
This is a short tutorial on the LaneRuler software suite. The core module is a command line c program, whose result can be reviewed and corrected using a java interface. The tutorial will go through the flow of the program, various flags for specifying the format of the gel, and details about all the options available.
![Lane tracking result for a sample DNA fingerprinting gel Lane tracking result for a sample DNA fingerprinting gel](http://plone.bcgsc.ca/platform/bioinfo/docs/laneruler/production.png/image_thumb)
Lane tracking result for a sample DNA fingerprinting gel
Ran with default parameters. Function call: >findlanes -p <project_directory>
![Sample lane tracking result for a PCR gel. Sample lane tracking result for a PCR gel.](http://plone.bcgsc.ca/platform/bioinfo/docs/laneruler/PCRgel.png/image_thumb)
Sample lane tracking result for a PCR gel.
Due to low data density, toneadjustment was turned off. Function call: >findlanes -p <project_directory> -a
![Sample lane tracking result for a cDNA gel. Sample lane tracking result for a cDNA gel.](http://plone.bcgsc.ca/platform/bioinfo/docs/laneruler/cDNAsample.png/image_thumb)
Sample lane tracking result for a cDNA gel.
A rotation was required as the gel initially had wells at top edge of the image. Due to low number of marker lanes, we match all peaks in all zones (-i). Tone adjustment was not done due to high data signal (-a). The morphology element size was adjusted since the marker band separation to image width ratio has changed significantly. Function call: >findlanes --numlanes 11 --markerperiod 10 --orientation 1 -a -i --morphelement 150