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Adjusting the Quality Values

Each base has its own quality value. Assembly will allow only values between 1 and 99 inclusive. A quality value of 0 means that this base should be ignored. A quality value of 100 means that this base is definitely correct and the consensus will be forced to be the same base type and will be given a consensus confidence of 100. If two conflicting bases both have a quality of 100 the consensus will be a dash with a confidence of 0.

Newly added bases or replaced bases are assigned a quality of 100.

Several keyboard commands are available to edit the quality value of an individual base.

 [                        Set quality to 0 and move cursor right
 ]                        Set quality to 100 and move cursor right
 Shift   Up-Arrow         Increment quality by 1
 Control Up-Arrow         Increment quality by 10
 Shift   Down-Arrow       Decrement quality by 1
 Control Down-Arrow       Decrement quality by 10

Finally note that quality values can also be made visible by clicking on the "Quality" checkbutton at the top of the editor. This shows the quality by use of a grey scale.

Adjusting the alignment coordinates

On rare occasions we may need to move an entire sequence a small amount to achieve an optimal alignment, rather than simply inserting or deleting pads.

This is achieved by using Control plus the left and right arrow keys while the editing cursor is anywhere on the sequence.

 Control Left-Arrow       Shift sequence left
 Control Right-Arrow      Shift sequence right

Adjusting the Cutoff Data

Sequences typically consist of a good quality "used" portion and poor quality "clipped" or "cutoff" portions at the 5' and 3' ends of the sequence. Although for short sequencing technologies it's quite likely we have no cutoff data at all. The reason for this is that the low quality ends of sequences may have a sufficient number of errors that the sequence alignment algorithms are no longer confident they have the correct bases aligned, or event that the sequence simply disagrees too much.

By default these are not shown, although you may see blank lines in the display as room is left for this sequence even when it is not visible. The cutoff data may be displayed by pressing the "Cutoffs" check-button at the top of the editor. The cutoff sequence will then be displayed in grey. We call the boundary between the cutoff data and the used data the cutoff position. These positions can be adjusted by pressing the "<" (left cutoff) or ">" (right cutoff) keys. In both cases the cutoff point is between the base with the editing cursor and the base to the left of the editing cursor.

Using the "<" and ">" keys with the editing cursor in the consensus performs bulk versions of these edits by clipping every single sequence to that poinit. One small difference here though is that the bulk versions only ever shrink cutoff data and do not grow it.

 <                        In sequence: set left cutoff position
 >                        In sequence: set right cutoff position

 <                        In consensus: bulk clip left cutoff
 >                        In consensus: bulk clip right cutoff

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Last generated on 25 November 2011.