ArticleMethods in molecular biology (Clifton, N.J.)2024
Plant Transcriptome Analysis with HISAT-StringTie-Ballgown and TopHat-Cufflinks Pipelines.
Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Genome-Wide Identification of thePlants (Basel, Switzerland) · 2026Article
- Identification and functional analysis of the SET domain-containing gene family in Cordyceps militaris.Scientific reports · 2025Article
- Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L.BMC genomics · 2025Article
- Article
- Transcriptome analysis revealed that AcWRKY75 transcription factor reduced the resistance of kiwifruit toFrontiers in plant science · 2024Article
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1 author.
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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.
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