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 Bioljournal_title
Genome biologyauthors
Davidson NM,Hawkins ADK,Oshlack Adoi
10.1186/s13059-017-1284-1subject
Has Abstractpub_date
2017-08-04 00:00:00pages
148issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-017-1284-1journal_volume
18pub_type
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