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. |
||||||
|
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 |
|
|
||||||
|
aThere were 9,491,394 pairs of reads classified as junction pairs. bThere were 2,702,624 pairs containing short-anchored reads. |
||||||
|
Kim et al. Genome Biology 2013 14:R36 doi:10.1186/gb-2013-14-4-r36 |
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