Table 2

Sources of false positive junction detection
Type of error False positives Qualitative filtering strategy Removed by qualitative filtering1 Removed by quantitative filtering2
False alignment to minor form 36.4% Remove novel minor forms 36.4% 30.7%
Incorrect strand 31.6% Inconsistency with gene model 31.6% 28.8%
Shifted on same strand 13.8% None 0% 12.2%
Paralog joining 8.5% Inconsistency with gene model 8.5% 7.7%
Repeat sequence induced 7.7% Exon-intron sequence similarity 7.7% 6.5%
Unidentified error 2% None 0% 0%
Total defined errors: 100% Total removed errors: 84.2% 75.9%

1False positives removed by Spanki’s qualitative filtering.

2False positives removed by filtering on entropy score (≥ 2), calculated by Spanki.

Sturgill et al.

Sturgill et al. BMC Bioinformatics 2013 14:320   doi:10.1186/1471-2105-14-320

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