通过长读测序进行转录本鉴定。

Transcript Identification Through Long-Read Sequencing.

机构信息

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.

Ono Pharmaceutical Co., Ltd., Osaka, Osaka, Japan.

出版信息

Methods Mol Biol. 2021;2284:531-541. doi: 10.1007/978-1-0716-1307-8_29.

DOI:10.1007/978-1-0716-1307-8_29

PMID:33835462

Abstract

RNA-seq using long-read sequencing, such as nanopore and SMRT (Single Molecule, Real-Time) sequencing, enabled the identification of the full-length structure of RNA molecules. Several tools for long-read RNA-seq were developed recently. In this section, we introduce an analytical pipeline of long-read RNA-seq for isoform identification and the estimation of expression levels using minimap2, TranscriptClean, and TALON. We applied this pipeline to the public direct RNA-seq data of the HAP1 and HEK293 cell lines to identify transcript isoforms which can be detected only using long-read RNA-seq data.

摘要

使用长读测序（如纳米孔和 SMRT（单分子实时）测序）进行 RNA-seq，可以鉴定 RNA 分子的全长结构。最近开发了几种用于长读 RNA-seq 的工具。在本节中，我们介绍了一种使用 minimap2、TranscriptClean 和 TALON 进行长读 RNA-seq 分析的流程，用于鉴定只有使用长读 RNA-seq 数据才能检测到的转录本异构体。我们将该流程应用于 HAP1 和 HEK293 细胞系的公共直接 RNA-seq 数据，以鉴定只能使用长读 RNA-seq 数据检测到的转录本异构体。