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Editing

Editing can take up a significant portion of the time taken in finishing a sequencing project. Gap4 has a selection of searches (see section Searching) designed to speed up this process. In general it is true that the problems that require most attention are conflicts between good bases. It may not be worthwhile editing all disagreeing bases as generally this will amount to adjusting poor quality data to agree with good quality data, in which case the consensus algorithm should be correct anyway.

Pads could also not be considered problems requiring edits. It is possible to output the consensus sequence (from the main Gap4 File menu) with pads stripped out. Obviously poorly defined pads (a mixture of several pads and several real bases) require checking in the same manner as other poorly defined consensus bases.

If you wish to check all base conflicts set the consensus algorithm to Frequency (see section The Consensus Calculation) and the consensus cutoff to 100. The consensus will then be a dash in all places where there is not a 100% agreement in the sequences. The "Next Problem" editor button will then step one at a time through each conflict.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_48.html