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FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity.
Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a semi-supervised anomaly detection strategy based on logistic regression. Multiple mapping reads with a unique location after filtering are rescued and reallocated to the most reliable candidate location.
FineSplice requires Python 2.x (>= 2.6) with the following modules installed: pysam (http://code.google.com/p/pysam/) and scikit-learn (http://scikit-learn.org/).
For further details check out our publication: Nucl. Acids Res. (2014) doi: 10.1093/nar/gku166
Features
- Align with TopHat2 using transcript annotations for superior mapping performance
- Run FineSplice to get rid of unreliable gapped alignments and improve splice junction detection precision
- Outputs a confident set of exon-exon junctions with the corresponding read counts for downstream analyses
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