Read1 ACC*AGT*CGTA Read2 ACC*AGT*CGTA Read3 ACC*AGT*CGTA Read4 ACCCAGTCCG Read5 ACC*AGT*CGTA Consensus ACC*AGT*CGTA
This is identical to the first case, except we have two edits within
Read4 in close proximity. This is usually due to a poor quality
reading, which can be checked by examining the trace and confidence values.
Whilst we could continue to make edits in the normal fashion it may be wiser
to take another approach.
One technique is to adjust the cutoff data for Read4. By marking the
data as hidden, this portion of the reading will no longer be used for
producing the consensus. However we can only extend the cutoff data at one end
or the other; it is not possible to have "hidden" data part way through a
reading except by modifying its confidence. Note though that adjusting the
cutoff data may mean that we have no data for one strand, which should be
solved by extra experiments.
If the reading is poor quality along its entire length, then disassembly is also a viable option. Using Highlight Disagreements ( see section Highlight Disagreements. ) or Check Assembly (see section Check Assembly) is a good way of finding such readings. Note that disassembling readings may have other implications. It could cause a hole in the contig (in which case it will be broken in two) or it could cause a single stranded segment. If this is the case, the user needs to weigh up the work involved with making many edits along the length of this reading against performing another experiment to obtain better quality data.