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Gelfinalisation configuration

This configuration keyword defines the program which combines the results of the gel analysis into data-files for further analysis.

These datafiles are designed to be analyzed further by programs such as FPC.

This program is called when the gel is finished (by stepping forward) in step 4 using the right-arrow button.

Command line arguments

The program needs only 2 command line arguments to find all the Image datafile previously written and combine them into a set of data-files for further analysis.

The configured command line for $gelfinalisation is :

amStep5 $gelpath $projectname

The gelfinalisation algorithm

The amStep5 program normalizes the sample band positions and writes 2 or 3 output files in the geldirectory.

  • $projname.$gelname.gel
  • $gelname.bands
  • $gelname.sizes (optional output file)

Where $projname and $gelname are parameters from the info file in the given $gelpath directory.

The sizes file can only be written if the standard file contains the optional 4th column containing the molecular sizes of each marker fragment.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/cpf6k9q6