[Up - Step 4 - Edit markerlock]
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>.sizeswhen 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
