The contig comparator is used to plot all templates with readings that span contigs. That is, the lines drawn on the contig comparator are a visual representation of the relationship (orientation and overlap) between contigs. When a template spans more than two contigs, all the combinations of pairs of contigs are plotted. However such cases are uncommon.
The figure above shows a typical Contig Comparator plot which includes
several types of result in addition to those from Read Pair analysis.
The lines for the read-pairs
are, by default, shown in blue. The length of the line is the average
length of the two readings within the pair. The slope of the line represents
the relative orientation of the two readings. If they are both the same
orientation (including both complemented) the line is drawn from top left to
bottom right, otherwise the line is drawn from top right to bottom left.
Clicking with the right mouse button on a read pair line brings up a
menu containing, amongst other things, "Invoke join editor"
(see section The Join Editor). This will
bring up the Join Editor with the two contigs shown end to end.
(Click for full size image)
Last generated on 25 November 2011.