[Up - Builtin Configuration]

Lanetracking configuration

This configuration keyword defines the program which performs the lane tracking for a given gel.

The lane grid is required when the gel processing gets to step 2. They are read from a lanes file. If it doesn't already exist the lanetracking program is called.

Command line arguments

The user/administrator has a choice of 2 different lanetracking program that can be used with Image. Each one has strengths in dealing with particular types of gels.

1. configuring Pathfinder

This program was originally conceived to perform lanetracking of ABI sequencing gels. It has been adapted to write a lanes file, so it works well within Image to process ABI gel-files.

The configured pathfinder command line for $lanetracking is :

pathfinder -i $lanenumber $markerrepeat $estimated-lanewidth $zonenumber $hi-res-imagefile $gelpath/lanes

2. configuring amStep2

This is the original lanetracker used on 8-Bit images scanned on the Amersham scanner. It is not suitable for 16-Bit images from ABI-gel files or the FluorImager. However it can still be configured as the lanetracker to be backwards compatible.

The configured amStep2 command line for $lanetracking is :

amStep2 -b $bgs-iteration -w $bgs-winsize-percentage $gelpath

It may be useful to include the complete directory path to the pathfinder or amStep2 executable to resolve ambiguities caused by different $PATH values in the shell-setup for different users.

The lanetracking algorithm

Refer to the relevant page on the web-site.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/pdywgb4v