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 transc...
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doaj-c21c8304183f45da8eb07ba74a1108372020-11-25T02:31:02ZengBMCGenome Biology1474-760X2017-08-0118111010.1186/s13059-017-1284-1SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomesNadia M. Davidson0Anthony D. K. Hawkins1Alicia Oshlack2Murdoch Children’s Research Institute, Royal Children’s HospitalMurdoch Children’s Research Institute, Royal Children’s HospitalMurdoch Children’s Research Institute, Royal Children’s HospitalAbstract 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.http://link.springer.com/article/10.1186/s13059-017-1284-1 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Nadia M. Davidson Anthony D. K. Hawkins Alicia Oshlack |
spellingShingle |
Nadia M. Davidson Anthony D. K. Hawkins Alicia Oshlack SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes Genome Biology |
author_facet |
Nadia M. Davidson Anthony D. K. Hawkins Alicia Oshlack |
author_sort |
Nadia M. Davidson |
title |
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes |
title_short |
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes |
title_full |
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes |
title_fullStr |
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes |
title_full_unstemmed |
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes |
title_sort |
supertranscripts: a data driven reference for analysis and visualisation of transcriptomes |
publisher |
BMC |
series |
Genome Biology |
issn |
1474-760X |
publishDate |
2017-08-01 |
description |
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. |
url |
http://link.springer.com/article/10.1186/s13059-017-1284-1 |
work_keys_str_mv |
AT nadiamdavidson supertranscriptsadatadrivenreferenceforanalysisandvisualisationoftranscriptomes AT anthonydkhawkins supertranscriptsadatadrivenreferenceforanalysisandvisualisationoftranscriptomes AT aliciaoshlack supertranscriptsadatadrivenreferenceforanalysisandvisualisationoftranscriptomes |
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1724825761005699072 |