Additional file 12.

Figure S3 - stitching segments to produce a full read alignment. (a) The segment in the third row for segment 1 and the one in the first row for segment 2 are connected because they are on the same chromosome (i) in the forward direction and with adjacent coordinates. These are then matched to the second row in segment 3 and glued together, producing the full-length read alignment at the bottom. (b) TopHat-Fusion tries to connect the segment in the second row for segment 1 with segments in the first and second rows for segment 2, but neither succeeds. Case 1 would require two fusion points in the same read, and case 2 cannot be fused with consistent coordinates. (c) Attempts to connect the segment in the second row for segment 2 with the one in the first row in segment 3: in case 3, there is no intron available, there is no fusion in case 4, and case 5 would require more than one fusion.

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Kim and Salzberg Genome Biology 2011 12:R72   doi:10.1186/gb-2011-12-8-r72