SpliceGrapher – Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data

splicegrapher

SpliceGrapher is a package for creating splice graphs from RNA-Seq data, guided by gene models and EST data (when available).

Features

  • Use your favorite read mapping and spliced alignment tools.
  • Accurate spliced-alignment filtering using SVM classifiers that recognize splice junction sequence features.
  • Generate statistics of alternative splicing.
  • Visualization of splice graphs, splice junctions, and read depth
  • Use our pipeline or construct your own custom pipeline out of SpliceGrapher modules.

Results obtained using RNA-Seq experiments in Arabidopsis thaliana show that predictions made by SpliceGrapher method are more consistent with current gene models than predictions made by TAU and Cufflinks. Furthermore, analysis of plant and human data indicates that the machine learning approach used by SpliceGrapher is useful for discriminating between real and spurious splice sites, and can improve the reliability of detection of alternative splicing.

SpliceGrapher is available for download at http://SpliceGrapher.sf.net.

  • Rogers MF, Thomas J, Reddy AS, Ben-Hur A. (2012) SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data. Genome Biol 13(1), R4. [abstract]