使用纳米孔测序分析叶绿体转录组第二部分：生物信息学分析和虚拟 RNA 印迹。

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

机构信息

Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France.

Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France.

出版信息

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

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

PMID:38502510

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.

摘要

纳米孔测序全长 cDNA 为质体 RNA 代谢提供了前所未有的详细信息。在生成纳米孔读取后，需要经过几个生物信息学步骤来分析数据。在本章中，我们将用几条简单的命令行描述读取的处理和映射，以及生成虚拟 Northern 印迹，作为一种简单而熟悉的方法来可视化纳米孔测序数据。