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The standard file

The standard file contains all the information about the standard marker bands that is needed for the marker locking and normalisation of the migration distances of the sample bands as they are observed on the gel.

This file is used to draw the pattern of the standard bands in Step 4. It is also used by the analysis components "markerlocking" (amStep4) and "gelfinalisation" (amStep5).

File format

The first line of the file contains the word "STANDARD" to identify the type of file. The rest of the file has one line per standard marker-band and each line has 3 or 4 columns.

original-master-distance
Positions of the marker bands on the original master gel. The gel positions of every sample band are mapped to this range to be comparable with other clones (however long ago they were fingerprinted) in the database. These values must never change during the lifetime of the mapping project.
actual-recent-distance
positions of the actual marker bands on a (fairly) recent gel. As the chemistry of gels may change slightly over the years, the marker bands may be observed in positions which are slightly from those on the original master gel. Although the values in the first columns must never change, these values in the second column can be adapted.
The marker-locking editor in Step 4 has a function (called "Merge into std" in the "File" menu) to perform this adaptation by blending in the currently observed coordinates into the values of the second column.
confidence-value
0.99 means that this band will always be there and must be matched and 0.01 means that it is highly unlikely that this band was called and might be ignored for matching.
(optional) fragment-size
Molecular size of that marker fragment. This information is only known in a few cases. If the sizes of each fragment becomes known, this information can be added in a text-editor.
If values are present in this column they are used to write a file called <gelnumber>.sizes when the gel is finished. This is an addition to the usual file <gelnumber>.bands (input data for fpc) which can be produced based on just 3 columns.

Example of a standardfile

This is an extract from a standardfile with size information.

  STANDARD
  0    69.0  0.9  1000000
  755  261   0.9  23130
  781  265   0.9  21226
  940  305.0 0.9  12216
  976  313.0 0.9  11198
  1018 323.0 0.9  10180
  1048 332.0 0.9  9416
  1071 334.6 0.9  9162
  1126 349.0 0.9  8144
  1195 368.0 0.9  7126
  1235 381.0 0.9  6557
  .
  .
  .
  2626 822.3 0.9  1018
  2684 839.8 0.9  947
  2764 870.0 0.9  831
  2982 948.0 0.9  564
  3029 965.3 0.9  517
  3147 1007.7 0.9 396
  3202 1027.3 0.9 344
  3252 1046.5 0.9 298
  3333 1088.7 0.9 220

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/8bhayy4j