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Table 2 Performance of TopHat2 and other spliced aligners on a set of 20 million pairs of 100-bp reads, simulated based on transcripts from the entire human genome.

From: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Program No. of mapped pairs Correctly mapped pairs, % Incorrectly mapped pairs, % Unmapped pairs, % Correct junction pairs, %a Correct short-anchored pairs, %b
TopHat2 + Bowtie1 19,683,426 96.70 1.72 1.58 93.31 90.09
TopHat2 + Bowtie2 19,686,006 96.19 2.24 1.57 92.03 85.88
TopHat1.14 19,219,055 89.57 6.53 3.90 78.36 40.39
GSNAP 19,999,867 88.84 11.16 0.00 76.55 22.87
RUM 19,869,579 79.07 20.28 0.65 56.28 8.42
MapSplice 19,342,087 92.03 4.68 3.29 86.53 72.48
STAR 19,951,620 85.21 14.55 0.24 68.94 3.16
  1. aThere were 9,491,394 pairs of reads classified as junction pairs.
  2. bThere were 2,702,624 pairs containing short-anchored reads.