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Table 4 Quality measures in detecting novel alternative splicing events on the simulated datasets with 5M and 10M reads

From: ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events

   5M 10M
Tool Measure ES A3 A5 IR ES A3 A5 IR
ASGAL Prec 0.997 0.955 0.905 0.862 0.995 0.938 0.895 0852
  Rec 0.917 0.741 0.737 0.674 0.963 0.789 0.781 0.681
  FM 0.955 0.835 0.812 0.756 0.979 0.857 0.834 0.757
SplAdder Prec 0.885 0.612 0.475 0.299 0.874 0.642 0.495 0.272
  Rec 0.802 0.884 0.821 0.531 0.848 0.925 0.891 0.521
  FM 0.841 0.723 0.602 0.383 0.860 0.758 0.637 0.357
rMATS Prec 0.996 - - - 0.997 - - -
  Rec 0.860 - - - 0.863 - - -
  FM 0.923 - - - 0.925 - - -
SUPPA2 Prec - - - - - - - -
  Rec - - - - - - - -
  FM - - - - - - - -
  1. Results obtained by ASGAL, SplAdder and rMATS (for which we used STAR to compute the alignments), and SUPPA2 (for which we used Salmon to obtain the transcript quantification) are reported. Precision (Prec), Recall (Rec), and F-Measure (FM) achieved on the simulated datasets in detecting novel alternative splicing events: exon skipping (ES), alternative acceptor site (A3), alternative donor site (A5), and intron retention (IR). A dash “-” means that the considered tool is not designed to detect that type of novel AS events