Table 2. Alignment accuracy on simulated PAR-CLIP data.

The most accurate alignment results were obtained for different parameter settings for each read aligner on 10 simulated PAR-CLIP datasets. The results are averaged per read aligner over all 10 datasets and are sorted by accuracy.

Aligner	Accuracy (in %)	Variance	Recall (in %)	Precision (in %)	Mapped overall	Mapped correctly	Real time (s)
PARA-suite pipeline	73.14	1.37E–06	84.49	71.85	1,024,792	969,948	396.8
BWA PARA	69.74	1.38E–06	82.16	68.24	975,672	924,802	153.7
BWA 2MMs	68.17	1.37E–06	82.31	64.98	959,171	904,034	359.2
Bowtie 2MMs	63.38	1.10E–06	77.91	60.93	886,512	840,540	120.6
BWA PSSM	59.80	1.18E–06	74.04	58.72	818,895	793,007	25.4
TopHat	59.69	8.35E–07	76.10	55.35	844,902	791,549	282.9
Bowtie2	56.22	1.11E–06	73.23	51.43	763,893	745,531	13.4
STAR	50.74	9.10E–07	69.57	43.02	826,871	672,920	248.6
MOSAIK	44.88	2.18E–04	62.83	37.16	897,679	595,220	12,128.18
Subjunc	35.42	9.03E–07	50.61	26.09	597,400	469,751	64.2