Bio-Rad EXQuest Spot Cutter - Manual (Page 295)

PDQuest User Guide
9-6
Select the Auto-select option to automatically select the best gels to cut from based on
spot quantity and quality. When you choose this option, the auto-selection parameters
will become available, and the gels will be selected in the table based on these
parameters.
Spot quantity usually varies among the gels in a MatchSet. In general, you want to cut
from gels in which spot quantity is higher (to get more sample). The Tolerance ratio is
used to determine the range of spot quantity that is acceptable when selecting which
gel to cut a particular spot from. If the quantity of a spot in only one gel falls within
the tolerance ratio, that gel will be auto-selected for the spot cut. However, if the
quantity of a spot in two or more gels falls within the tolerance ratio, then the auto-
select mechanism will consider which gel will best minimize the time and effort
required to switch gels on the spot cutter platform.
For example, say that you have five gels in a MatchSet, and with a tolerance ratio of 1
(the lowest setting) auto-selection specifies different cuts in all five gels, requiring to
you to change gels in the spot cutter five times. However, by increasing the tolerance
ratio slightly, auto-selection finds that three gels contain spots whose quantities fall
within the specified tolerance, and it adjusts the cuts so that only those three gels are
selected. This will save you considerable time and effort switching gels in the spot
cutter.
Check the Include Spot Quality box to consider spot quality when auto-selecting
spots. When this checkbox is selected, a well-resolved spot of sufficient quantity will
be favored over a less well-resolved spot of higher quantity (within the specified
tolerance ratio).
To make all the cuts from the same gel, select the Single Gel option button. Then
select the gel name from the pulldown box. All the cut requests listed in the table will
be located in that gel.
To choose gels and spots manually, click the Manual option button. The spots will
appear selected in the table based solely on quantity, and you can then click on which
spots to cut.
Table Options
The table in the Excision Gel Selection tool lists the spots in the analysis set (by
Standard Spot Number) and their quantities in the different gels. The columns are