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Guided Reconstruction of Full-Length Isoforms from Short Reads by CIDANE

  • Sandro Andreotti
  • Stefan Canzar
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1870)

Abstract

Alternative splicing allows genes to express isoforms with different coding or regulatory functions on demand. While short read deep sequencing technologies (RNA-seq) provide an immediate measurement of local splicing events, the phasing of these events along full-length isoforms requires the computational inference of long-range dependencies from short-range data points. We introduce CIDANE, a tool for the assembly and quantification of full-length isoforms from short read RNA-seq data. CIDANE bridges the gap between RNA quantification methods that rely on a complete annotation of a species’ transcriptome, and transcript assembly methods that will detect novel isoforms at the cost of a lower accuracy.

Key words

Transcript isoforms Alternative splicing RNA sequencing RNA assembly CIDANE 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Mathematics and Computer ScienceFreie Universität BerlinBerlinGermany
  2. 2.Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany

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