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Validation of Splicing Events in Transcriptome Sequencing Data.

Wolfgang Kaisers1,2, Johannes Ptok3, Holger Schwender4,5

  • 1Department for Anaesthesiology, University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany. kaisers@med.uni-duesseldorf.de.

International Journal of Molecular Sciences
|May 27, 2017
PubMed
Summary
This summary is machine-generated.

New quality scores, gap quality score (gqs) and weighted gap information score (wgis), effectively validate potential splice-sites identified from genomic alignments. These scores significantly reduce false discoveries from alignment algorithms like TopHat and STAR.

Keywords:
MaxEntRNA-seqSTARTopHatsplice sites

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Genomic alignments of messenger RNA reveal gapped alignments, indicating intron removal.
  • These gap-sites are potential splice-site landmarks but are reported with a high false discovery rate by alignment algorithms.
  • Validation methods are crucial to accurately identify true splice-sites.

Purpose of the Study:

  • To introduce and evaluate two novel quality scores, gap quality score (gqs) and weighted gap information score (wgis), for validating putative splicing events.
  • To assess the effectiveness of gqs and wgis in reducing false discovery rates of splice-sites identified by TopHat and STAR aligners.

Main Methods:

  • FASTQ files from 54 human dermal fibroblast samples were aligned to the human genome (GRCh38) using TopHat and STAR.
  • Two quality scores, gqs and wgis, were developed: gqs uses alignment data, while wgis incorporates genomic sequence information.
  • Statistical properties of validated gap-sites were analyzed for similarity to known exon-intron borders.

Main Results:

  • TopHat identified 1,000,380 gap-sites and STAR identified 6,487,577 across 54 samples.
  • Validation with gqs yielded 156,251 (TopHat) and 166,294 (STAR) gap-sites.
  • Validation with wgis yielded 770,327 (TopHat) and 1,065,596 (STAR) gap-sites, significantly reducing false positives.

Conclusions:

  • Both TopHat and STAR aligners report gap-sites with a substantial false discovery rate.
  • The developed gqs and wgis scores provide effective validation for putative splice-sites.
  • Utilizing gqs and wgis can drastically improve the accuracy of splice-site identification in genomic analyses.