Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development
复制标题
DOI：
10.1093/bioinformatics/btx504
复制
发表时间：
2018-01-01
期刊：
影响因子：
5.8
通讯作者：
Wong, David T. W.
中科院分区：
文献类型：
--
作者：
Kaczor-Urbanowicz, Karolina Elzbieta;Kim, Yong;Wong, David T. W.
动机：分析人类唾液中的 RNA 测序 (RNA-Seq) 数据具有挑战性。生物信息学程序缺乏标准化和统一会削弱唾液的诊断潜力。因此，它激励我们进行这项研究。结果：我们应用主要流程对 98 名健康韩国志愿者唾液的小 RNA-Seq 数据进行生物信息学分析，包括使用 Bowtie1 将读数直接或间接映射到人类基因组。通过另一个管道对外源基因组的比对分析表明，几乎所有的读数都映射到细菌基因组。因此，唾液 exRNA 具有基本特性，保证在进行生物信息学分析时设计独特的附加步骤。我们的流程可以作为处理人类唾液 RNA-Seq 数据的潜在指南。 可用性和实施：exceRpt (v4.6.3) 小 RNA-seq 流程 (github.gersteinlab.org/exceRpt) 生成的实验数据的处理和分析结果可从 exRNA atlas (exrna-atlas.org) 获取。本文使用外源基因组比对及其定量结果来分析外源来源的小RNA。联系方式：dtww@ucla.edu
Motivation: Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study.Results: We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva.Availability and implementation: Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin.Contact: dtww@ucla.edu