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Editing

Editing can take up a significant portion of the time taken to finish a sequencing project. Gap5 has a selection of searches (see section Searching) designed to speed up this process. The problems that require most attention are conflicts between good bases. Where base confidence values are present it should be unnecessary to edit all conflicting bases as, generally, this will amount to adjusting poor quality data to agree with good quality data in which case the consensus sequence should be correct anyway.

Pads in the consensus should not be considered a problem requiring edits because it is possible to output the consensus sequence (from the main Gap5 File menu) with pads stripped out. Obviously poorly defined pads (a mixture of several alignment padding characters and real bases) require checking in the same manner as other poorly defined consensus bases.

To change a base simply overtype with a new base call, one of a,c,g or t in lowercase. Alternatively a base can be changed to an alignment padding character by pressing "*". These new bases and pads automatically get given a quality value of 100, but see below for how to adjust this. The consensus cannot be edited in this manner.

To insert a gap into sequence press "i" or the Insert key. At present only alignment pads can be inserted, not bases, although the pads can subsequently be edited to turn them into bases. The "i" and Insert keys also permits insertions of gaps into the consensus, which it achieves by inserting into every sequence aligned at that position.

Bases may be deleted by pressing the Delete or Backspace key. This deletes the base immediately to the left of the current editing cursor. Note that if Delete or Backspace is pressed with the editing cursor on the consensus this removes an entire column of data. Deleting anything other than alignment padding characters (either in sequences or the consensus) is a dangerous operation needing careful thought. To prevent accidental removal of data therefore, to delete anything other than "*" you must press Control in conjunction with Delete or Backspace.


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Last generated on 25 November 2011.