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. 2019 Jul 23;17(3):e26. doi: 10.5808/GI.2019.17.3.e26

Table 1.

Comparison of RNA-Seq alignment programs

Mapping program No. of correct alignments out of 269 known fusion transcriptsa
50 bp 75 bp 100 bp
GMAP 59 28 3
SSAHA2 237 248 252
Bowtie2 242 245 248
BWA 1 238 244
BLAT 218 225 226
TopHat2 227 228 226

All alignment tools were run with default options.

RNA-Seq, RNA sequencing.

a

Two hundred sixty-nine known fusion transcripts were collected from TICdb and ChimerDB 2.0.