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Table 3 The overlapping spliced junctions identified by TopHat and our RSR

From: Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

  mouse-Het mouse-KO mouse-Het mouse-KO human
Software 500 nM Thapsigargin (Tg) 1 mM Dithiothreitol (Dtt) ENCODE
TopHat 956 923 8897 7847 237,155
RSR 144 183 6727 6343 32,597
Common 38 41 2398 2128 314
Common/TopHat 3.97 % 4.44 % 26.95 % 27.12 % 0.13 %
Common/RSR 26.39 % 22.40 % 35.65 % 33.55 % 0.96 %