The Use of Nanopore Sequencing to Analyze the Chloroplast Transcriptome Part II: Bioinformatic Analyzes and Virtual RNA Blots

Etienne Delannoy; Arnaud Liehrmann; Benoît Castandet

doi:10.1007/978-1-0716-3726-5_16

The Use of Nanopore Sequencing to Analyze the Chloroplast Transcriptome Part II: Bioinformatic Analyzes and Virtual RNA Blots

Methods Mol Biol. 2024:2776:259-267. doi: 10.1007/978-1-0716-3726-5_16.

Authors

Etienne Delannoy^{1

2}, Arnaud Liehrmann^{3

4

5}, Benoît Castandet^{3

4}

Affiliations

¹ Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France. [email protected].
² Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France. [email protected].
³ Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France.
⁴ Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France.
⁵ Laboratoire de Mathématiques et de Modélisation d'Evry (LaMME), Université d'Evry-Val-d'Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry, France.

PMID: 38502510
DOI: 10.1007/978-1-0716-3726-5_16

Abstract

Nanopore sequencing of full-length cDNAs offers unprecedented details of the plastid RNA metabolism. After the generation of the nanopore reads, several bioinformatic steps are required to analyze the data. In this chapter, we describe in a few simple command lines the processing and mapping of the reads as well as the generation of virtual Northern blots as a simple and familiar way to visualize Nanopore sequencing data.

Keywords: Chloroplast; Nanopore sequencing; RNA-Seq; Virtual Northern blot.

MeSH terms

Chloroplasts / genetics
Computational Biology
High-Throughput Nucleotide Sequencing
Nanopore Sequencing*
RNA
Sequence Analysis, RNA
Transcriptome*

Substances

RNA