Table 2

Runtime

Datasets:

Validation

High-Throughput

RNA-seq reads

66 Million

145 Million

AS events

26

1051


Cufflinks

16 min

75 min

MISO

77 min

458 min


Preprocess

4 min

11 min

Gaussian

+1 sec

+2 min

Native

+2 sec

+5 min

Mixture

+6 sec

+17 min

Bootstrap

+12 sec

+29 min


Comparison of run times between different PSI estimation methods. For our methods, we report the runtime of the shared pre-processing step separately from the PSI estimation. All tests were performed on a Dell Precision T7400 workstation with 8 cores (at 3 GHz) and 32 GB of RAM. We report wall-clock times averaged over 3 re-runs then rounded to the nearest minute (or second where appropriate).

Kakaradov et al. BMC Bioinformatics 2012 13(Suppl 6):S11   doi:10.1186/1471-2105-13-S6-S11

Open Data