Plant Transcriptome Analysis with HISAT-StringTie-Ballgown and TopHat-Cufflinks Pipelines.
Methods Mol Biol
; 2812: 203-213, 2024.
Article
en En
| MEDLINE
| ID: mdl-39068364
ABSTRACT
The development of next-generation sequencing technology has led to a burst of data in a single assay. Management of a large dataset requires high demands on bioinformatic skills and computing resources. Here we present two popular pipelines for RNA-seq data analysis, using open-source software tools HISAT-StringTie-Ballgown and TopHat-Cufflinks. To meet the need of plant scientist, we describe in detail how to perform such comprehensive analysis beginning with raw RNA-seq reads and available reference genome. It allows biologists to align short reads to a reference genome, measure the transcript abundance, and analyze gene differential expression under two or more conditions. We also discuss other RNA-seq tools that are comparable or alternative to this protocol.
Palabras clave
Texto completo:
1
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
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Biología Computacional
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Perfilación de la Expresión Génica
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Secuenciación de Nucleótidos de Alto Rendimiento
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Transcriptoma
Idioma:
En
Revista:
Methods Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2024
Tipo del documento:
Article
País de afiliación:
China