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The norm-fac file

When all marker bands are lined up with their respective standard bands and all sample bands have been confirmed the gel can be finished. In order to mormalise the migration distances of the sample bands to the scale of a uniform standard gel a set of normalisation factors is calculated for every gel when it is finished. These factors describes the positioning of the actual marker bands on the current gel in relation to the standard bands (which were derived from a master gel). These factors are used by the gelfinalisation step to produce a normalised .bands-file.

Note that the factors can only be written when every marker lane contains exactly as many bands as the standard file.

File format

The normalisation factors are stored in a file called "norm-fac" in the gel-directory.

The first line of the file contains the word "NORMFACTORS".

The normalisation factors are written in blocks - one block per marker lane. The first line in a block is the number of bands in that lane, followed by that many lines - one for each marker band. Because of the restriction that on completion of step 4 every marker lane has to have as many bands as there are in the standard file, the blocks will all be of equal sizes. The number that describes the length of each block will be the same for the blocks of every marker lane.

Each block has 3 or 4 columns - one line is written for each marker band in the lane. The bands are written left to right (starting with the lowest migration distance - independent of the "lockdirection" parameter). The numbers in the 3 or 4 columns are :

lane-number
of this marker lane, starting with 0 going up in steps of size "marker repeat".
standard-band-distance
original migration distance of the corresponding standard band. This is the number from the 1st column of the standard file of the band lined up to the marker band in the line-up shown in step 4.
actual-band-distance
actual migration distance of this marker band on the current gel. This is the x-coordinate number shown in the statusbar in the step 4 display when the band is selected.
(optional) standard-fragment-size
Molecular size of the corresponding standard band. This value is only available if the standard file has an optional fourth column.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/kywxtg1f