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Template Status

This option allows control over computation of the template status. The validity of a template is computed by checking the size (based on the locations of assembled readings and position of vector tags) and the orientation of sequences (based on their "primer type" values).

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The most likely item to need changing is the "size limit scale factor". The expected range of template sizes for a ligation are specified in each template record as a minimum-to-maximum range. Gap4 takes a very simple approach as anything within this range is valid and anything outside it is invalid. The scale factor is applied such that the maximum range becomes "max * scale" and the minimum range becomes "min / scale". So a scale factor of 2 would adjust a range from 1.0-1.4Kb to 0.5-2.8Kb.

The "minimum valid vector tag length" is designed to workaround problems where some assemblies end up with SVEC tags of 1 or 2 bases long (which are common when converting from phrap for some reason). The start and end of a template may be derived from observing a single reading with sequencing vector at both ends, so the presence of very short falsely added SVEC tags will mark many templates as inconsistent.

The "Ignore all primer-type values" and "Ignore custom primer-type values" are methods to disable Gap4's trust in the primer type information for each sequence. Normally this will be one of universal-forward, universal-reverse, custom-forward (e.g. from a primer-walk) and custom-reverse.


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Last generated on 25 November 2011.