Supplementary Tables

34 downloads 0 Views 296KB Size Report
0.1 5.09 2.80 92.11 2.80 1.02 18.39 80.59 2.68 10.34 3.06 86.60 6.62 1.81 11.33 86.86 292.00 3.35 4.96 91.69 24.20. 50. 1 5.59 4.46 89.95 3.90 1.10 24.40 ...
Highly sensitive and ultrafast read mapping for RNA-seq analysis Medina, I., Tárraga, J., Martínez, H., Barrachina, S., Castillo, M.I., Paschall, J., Salavert-Torres, J., Blanquer-Espert, I., Hernández-García, V., Quintana-Ortí, E.S. & Dopazo, J.

Supplementary Tables

Supplementary Table 1. Benchmarking for the simulated dataset containing 10 million single-end reads simulated with the dwgsim program. First column, RL, indicated read length in bps. Second column represents the mutation rate (MR). For each program the table contains the following columns with the percentages of: IMR: incorrectly mapped reads, RNM: reads not mapped, CMR: correctly mapped reads covering the corresponding splice junctions. The last column, T, represent runtimes to produce a BAM file in minutes. HPG Aligner 1 RL 50

75

100

150

250

400

MR 0.1 1 2 0.1 1 2 0.1 1 2 0.1 1 2 0.1 1 2 0.1 1 2

IMR 5.09 5.59 6.86 4.50 5.26 6.26 4.13 4.92 5.96 4.27 5.08 6.02 4.09 4.87 6.42 3.98 4.89 6.51

RNM 2.80 4.46 6.31 0.61 1.17 2.30 0.34 0.65 1.42 0.40 0.78 1.43 0.70 1.66 3.15 1.23 3.37 6.59

CMR 92.11 89.95 86.83 94.89 93.57 91.44 95.53 94.43 92.62 95.33 94.14 92.55 95.21 93.47 90.43 94.79 91.74 86.90

HISAT T 2.80 3.90 3.60 3.80 3.60 5.00 5.30 5.60 5.50 5.90 6.50 6.00 9.00 9.30 8.00 9.60 10.00 12.80

IMR 1.02 1.10 1.14 0.58 0.60 0.60 0.43 0.46 0.44 0.34 0.31 0.16 0.15 0.10 0.04 0.02 0.01 0.00

RNM 18.39 24.40 31.22 8.19 13.60 20.98 8.90 16.00 25.85 15.13 28.65 45.27 39.01 63.40 82.18 78.75 93.82 98.78

CMR 80.59 74.5 67.64 91.23 85.8 78.42 90.67 83.54 73.71 84.53 71.04 54.57 60.84 36.5 17.78 21.23 6.17 1.22

STAR 2 T 2.68 2.74 2.83 3.10 3.20 3.28 3.97 4.18 4.16 5.26 5.13 5.14 6.38 4.28 6.00 8.06 8.11 8.31

IMR 10.34 10.44 10.43 11.91 12.44 12.77 11.94 12.67 13.19 12.38 13.38 15.33 11.38 13.76 16.90 14.30 18.28 22.23

RNM 3.06 4.98 7.64 1.36 2.64 4.53 0.98 2.24 4.14 0.53 1.54 3.26 0.63 2.09 5.08 1.57 6.56 18.59

CMR 86.60 84.58 81.93 86.73 84.92 82.70 87.08 85.09 82.67 87.09 85.08 81.41 87.99 84.15 78.02 84.13 75.16 59.18

TopHat 2 + Bowtie 2 T 6.62 6.90 10.90 6.83 6.60 10.50 7.75 7.08 10.20 8.18 9.07 13.00 11.95 12.33 16.70 19.40 20.20 21.40

IMR 1.81 1.70 1.57 1.08 0.92 0.76 0.72 0.57 0.43 0.35 0.23 0.10 0.08 0.04 0.01 0.02 0.00 0.00

RNM 11.33 18.37 27.14 22.90 35.19 48.42 36.71 52.44 66.93 62.07 77.82 88.56 89.67 96.55 99.06 99.00 99.87 99.99

CMR 86.86 79.93 71.29 76.02 63.89 50.82 62.57 46.99 32.64 37.58 21.95 11.34 10.25 3.41 0.93 0.98 0.13 0.01

T 292.00 395.00 443.00 53.50 54.30 56.00 75.20 80.30 85.50 130.60 142.40 84.50 252.00 208.00 155.00 374.20 382.40 271.00

MapSplice 2 IMR RNM 3.35 4.96 3.27 8.88 3.17 14.01 5.46 1.45 6.90 3.35 8.57 6.48 7.48 0.58 11.75 1.33 16.05 2.63 19.87 0.69 25.53 1.06 21.49 1.54 42.49 0.26 47.02 0.32 40.22 0.38 56.35 0.04 57.41 0.05 56.83 0.05

CMR 91.69 87.85 82.82 93.09 89.75 84.95 91.94 86.92 81.32 79.44 73.41 76.97 57.25 52.66 59.40 43.61 42.54 43.12

T 24.20 23.70 25.40 29.60 28.50 32.10 36.40 38.30 40.15 47.50 47.00 43.40 61.95 62.20 58.40 81.10 83.00 85.20

Supplementary Table 2. Benchmarking for the simulated dataset containing 10 million paired-end reads simulated with the dwgsim program. First column, RL, indicated read length in bps. Second column represents the mutation rate (MR). For each program the table contains the following columns with the percentages of: IMR: incorrectly mapped reads, RNM: reads not mapped, CMR: correctly mapped reads covering the corresponding splice junctions. The last column, T, represent runtimes to produce a BAM file in minutes.

RL 50 75 100 150 250 400

MR 0.1 1 0.1 1 0.1 1 0.1 1 0.1 1 0.1 1

IMR 4.23 4.49 3.89 4.48 3.68 4.38 4.02 4.87 4.08 4.95 3.99 4.96

HPG Aligner 1 RNM CMR 5.03 90.74 6.33 89.18 1.66 94.45 2.19 93.33 1.45 94.87 1.35 94.27 0.82 95.16 1.21 93.92 0.96 94.96 1.91 93.14 1.41 94.60 3.60 91.44

T 5.50 5.90 6.10 7.00 7.40 8.30 10.10 10.50 11.70 17.90 16.00 19.00

IMR 1.02 1.14 0.59 0.64 0.51 0.53 0.4 0.36 0.18 0.11 0.03 0.01

HISAT RNM CMR 6.44 92.54 10.21 88.65 5.70 93.71 10.00 89.36 7.54 91.95 14.33 85.14 14.40 85.20 28.38 71.26 39.63 60.19 64.33 35.56 79.44 20.53 94.06 5.93

T 5.72 5.86 6.54 6.60 8.38 8.52 10.53 10.67 13.71 13.51 18.02 17.86

IMR 10.92 10.87 12.81 13.69 13.18 14.17 13.09 15.02 16.33 19.98 22.30 13.85

STAR 2 RNM CMR 7.25 81.83 10.96 78.17 1.14 86.05 2.13 84.18 1.19 85.63 1.14 84.69 0.26 86.65 0.89 84.09 1.81 81.86 8.45 71.57 24.15 53.55 56.28 29.87

T 8.10 8.05 9.13 9.55 11.17 12.18 14.87 15.62 25.40 26.47 78.20 82.70

IMR 1.17 1.04 0.67 0.53 0.47 0.34 0.25 0.16 0.06 0.03 0.01 0.01

TopHat 2 + Bowtie 2 RNM CMR T 15.00 83.83 702.30 23.83 75.13 848.20 33.26 66.07 107.00 47.40 52.07 110.00 48.73 50.80 151.80 63.56 36.10 161.80 70.37 29.38 253.00 82.38 17.46 277.35 91.13 8.81 506.50 96.80 3.17 541.00 99.03 0.96 751.20 99.86 0.13 778.00

IMR 3.03 3.33 4.84 6.15 6.62 9.12 14.63 19.37 35.71 39.80 52.48 53.54

MapSplice 2 RNM CMR 4.80 92.17 8.33 88.34 1.39 93.77 3.02 90.83 0.74 92.64 1.26 89.62 0.73 84.64 1.10 79.53 0.95 63.34 1.05 59.15 1.56 45.96 1.53 44.93

T 48.20 49.20 60.80 62.50 73.40 76.70 91.50 95.10 130.70 126.90 179.10 117.90