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. 2024:2812:203-213.
doi: 10.1007/978-1-0716-3886-6_11.

Plant Transcriptome Analysis with HISAT-StringTie-Ballgown and TopHat-Cufflinks Pipelines

Xiaolan Rao  1
Affiliations

Plant Transcriptome Analysis with HISAT-StringTie-Ballgown and TopHat-Cufflinks Pipelines

Xiaolan Rao. Methods Mol Biol. 2024.

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.

Keywords: Ballgown; Cufflinks; Differential gene expression; Gene expression; HISAT; RNA-seq; StringTie; TopHat; Transcriptome.

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References

    1. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63. https://doi.org/10.1038/nrg2484 - DOI - PubMed - PMC
    1. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523–536. https://doi.org/10.1016/j.cell.2008.03.029 - DOI - PubMed - PMC
    1. Stark R, Grzelak M, Hadfield J (2019) RNA sequencing: the teenage years. Nat Rev Genet 20(11):631–656. https://doi.org/10.1038/s41576-019-0150-2 - DOI - PubMed
    1. Martin LB, Fei Z, Giovannoni JJ, Rose JK (2013) Catalyzing plant science research with RNA-seq. Front Plant Sci 4:66. https://doi.org/10.3389/fpls.2013.00066 - DOI - PubMed - PMC
    1. Garber M, Grabherr MG, Guttman M, Trapnell C (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8(6):469–477. https://doi.org/10.1038/nmeth.1613 - DOI - PubMed

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