期刊
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
卷 78, 期 19, 页码 6812-6818出版社
AMER SOC MICROBIOLOGY
DOI: 10.1128/AEM.01418-12
关键词
-
资金
- Office of Science (BER)
- U.S. Department of Energy [DE-FG02-08ER64482]
- National Institutes of Health, National Institute of Allergy and Infectious Diseases [U54 AI057141]
- Japan Society for the Promotion of Science (JSPS)
- Uehara Memorial Foundation
- Cell Science Research Foundation
High-throughput sequencing of cDNA prepared from RNA, an approach known as RNA-seq, is coming into increasing use as a method for transcriptome analysis. Despite its many advantages, widespread adoption of the technique has been hampered by a lack of easy-to-use, integrated, open-source tools for analyzing the nucleotide sequence data that are generated. Here we describe Xpression, an integrated tool for processing prokaryotic RNA-seq data. The tool is easy to use and is fully automated. It performs all essential processing tasks, including nucleotide sequence extraction, alignment, quantification, normalization, and visualization. Importantly, Xpression processes multiplexed and strand-specific nucleotide sequence data. It extracts and trims specific sequences from files and separately quantifies sense and antisense reads in the final results. Outputs from the tool can also be conveniently used in downstream analysis. In this paper, we show the utility of Xpression to process strand-specific RNA-seq data to identify genes regulated by CouR, a transcription factor that controls p-coumarate degradation by the bacterium Rhodopseudomonas palustris.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据