SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes.

Abstract:

:Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a single sequence. The Lace software is provided to construct superTranscripts from any set of transcripts, including de novo assemblies. We demonstrate how superTranscripts enable visualisation, variant detection and differential isoform detection in non-model organisms. We further use Lace to combine reference and assembled transcriptomes for chicken and recover hundreds of gaps in the reference genome.

journal_name

Genome Biol

journal_title

Genome biology

authors

Davidson NM,Hawkins ADK,Oshlack A

doi

10.1186/s13059-017-1284-1

subject

Has Abstract

pub_date

2017-08-04 00:00:00

pages

148

issue

1

eissn

1474-7596

issn

1474-760X

pii

10.1186/s13059-017-1284-1

journal_volume

18

pub_type

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