[Up - Builtin Configuration]

Markerlocking configuration

This configuration keyword defines the program helps the user to perform marker locking at the analysis Step 4. Once the user has lined up the bands in one marker lane with the standard bands, it will perform the same type of editing in all the other lanes, therefore greatly reducing the editing time across the gel.

The markerlocking program is called when the user presses the button re-lock on lane in Step 4. The line-up of marker bands to their standards is required to finalise a gel.

Command line arguments

The markerlocking program is called amStep4. The program has two command line options, if it was run by hand from a command shell window directly. But only one of those parameters is statically configurable. The other command line option is dynamically assigned by the program when it is launched from within step 4. It specifies the currently selected lane to lock on to.

The configurable 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 $markerlocking is :

amStep4 $gelpath

The option to specify the current lane to use for locking is specified with the -L command line option. If the user has activated lane number 0 in step 4 and presses the [re-lock on lane] button, the following command will be executed :

amStep4 -L 0 $gelpath

Where $gelpath is of course substituted for the gelpath value in the info file of the current gel.

It may be useful to include the complete directory path to the amStep4 executable to resolve ambiguities caused by different $PATH values in the shell-setup for different users.

The markerlocking algorithm

Refer to the relevant page on the web-site.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/07lc2ltp