Dec 13, 2018

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

Methods in Molecular Biology
Sandro Andreotti, Stefan Canzar

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.

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Mentioned in this Paper

Nested Transcripts
Genes
Workflow
Reconstructive Surgical Procedures
RNA Isoforms
Genome Mapping
Computer Programs and Programming
Gene Function
Deep Sequencing
RNA Splicing

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