[Up - Builtin Configuration]

Bandcalling configuration

This configuration keyword defines the program which performs the band calling and calculates the band data for a given gel.

The bands are required when the gel processing gets to step 3. They are read from a raw-bands file. If it doesn't already exist the bandcalling program is called.

Command line arguments

The bandcaller is called amStep3. It's only command line argument is the gelpath. The program will extract all necessary gel-parameters from the info file in the given directory.

The configured command line for $bandcalling is:

amStep3 $gelpath 

It may be useful to include the complete directory path to the amStep3 executable to resolve ambiguities caused by different $PATH values in the shell-setup for different users.

The bandcalling algorithm

Refer to the relevant page on the web-site.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/609qvyru