Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq Data Using SplAdder.
Methods Mol Biol
; 2493: 167-193, 2022.
Article
en En
| MEDLINE
| ID: mdl-35751815
ABSTRACT
Alternative splicing (AS) is a regulatory process during mRNA maturation that shapes higher eukaryotes' complex transcriptomes. High-throughput sequencing of RNA (RNA-Seq) allows for measurements of AS transcripts at an unprecedented depth and diversity. The ever-expanding catalog of known AS events provides biological insights into gene regulation, population genetics, or in the context of disease. Here, we present an overview on the usage of SplAdder, a graph-based alternative splicing toolbox, which can integrate an arbitrarily large number of RNA-Seq alignments and a given annotation file to augment the shared annotation based on RNA-Seq evidence. The shared augmented annotation graph is then used to identify, quantify, and confirm alternative splicing events based on the RNA-Seq data. Splice graphs for individual alignments can also be tested for significant quantitative differences between other samples or groups of samples.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
ARN
/
Empalme Alternativo
Tipo de estudio:
Diagnostic_studies
Idioma:
En
Revista:
Methods Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2022
Tipo del documento:
Article
País de afiliación:
Suiza