利用 RNA-seq 分析工具 ANNOgesic 发现新型细菌小 RNA。

Discovering Novel Bacterial Small RNA by RNA-seq Analysis Toolkit ANNOgesic.

机构信息

Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.

Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.

出版信息

Methods Mol Biol. 2024;2741:35-69. doi: 10.1007/978-1-0716-3565-0_4.

DOI:10.1007/978-1-0716-3565-0_4

PMID:38217648

Abstract

ANNOgesic is an RNA-seq analysis pipeline that can detect sRNAs and many other genomic features in bacteria and archaea. In addition to listing sRNA candidates, ANNOgesic also generates various formats of data files for visual examination and downstream experimental design. Based on validations from previous studies, the sRNA predictions are accurate and reliable. In this chapter, we outline the sRNA detection algorithm, important parameters used, step-by-step execution, and data interpretation with a B. pertussis study as an example. Following those procedures, novel sRNA can be revealed by ANNOgesic.

摘要

ANNOgesic 是一个 RNA-seq 分析管道，可以在细菌和古菌中检测 sRNA 和许多其他基因组特征。除了列出 sRNA 候选物外，ANNOgesic 还生成各种格式的数据文件，用于可视化检查和下游实验设计。基于先前研究的验证，sRNA 预测是准确和可靠的。在本章中，我们以百日咳博德特氏菌研究为例，概述了 sRNA 检测算法、使用的重要参数、逐步执行和数据解释。按照这些步骤，ANNOgesic 可以揭示新的 sRNA。