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Table 1 Performance of TopHat2 and other spliced aligners on a set of 20 million 100-bp, single-end 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 reads Correctly mapped reads, % Incorrectly mapped reads, % Unmapped reads, % Correct junction reads, %a Correct short-anchored reads, %b
TopHat2 + Bowtie1 19,826,638 98.31 0.82 0.87 95.28 93.69
TopHat2 + Bowtie2 19,826,673 98.03 1.10 0.87 94.28 89.67
TopHat1.14 19,616,874 94.64 3.45 1.91 84.44 44.08
GSNAP 19,997,255 94.21 5.77 0.02 83.15 26.01
RUM 19,555,823 88.11 9.67 2.22 65.35 8.59
MapSplice 19,872,372 97.28 2.08 0.64 92.09 75.57
STAR 19,087,508 92.14 3.30 4.56 77.17 3.54
  1. aThere were 6,862,278 reads spanning one or more splice junctions; the alignment accuracy of junction reads refers to this set.
  2. bThere were 1,448,022 reads extending 10 bp or less into one exon; the alignment accuracy of the short-anchored reads is based on these alignments.