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- Title
ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species.
- Authors
Liu, Peng; Ewald, Jessica; Pang, Zhiqiang; Legrand, Elena; Jeon, Yeon Seon; Sangiovanni, Jonathan; Hacariz, Orcun; Zhou, Guangyan; Head, Jessica A.; Basu, Niladri; Xia, Jianguo
- Abstract
The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based platform for processing, analyzing, and interpreting RNA-sequencing data from any eukaryotic species. ExpressAnalyst contains a series of modules that cover from processing and annotation of FASTQ files to statistical and functional analysis of count tables or gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst allows researchers to obtain global expression profiles and gene-level insights from raw RNA-sequencing reads within 24 h. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-sequencing data from multiple non-model salamander species, including two that do not have a reference transcriptome. RNA-sequencing data analysis is difficult for non-model species that have no reference genome. ExpressAnalyst enables RNA-sequencing analysis for any eukaryotic species in less than 24 h, on a laptop, and without any programming.
- Subjects
RNA sequencing; SPECIES; FUNCTIONAL analysis; NON-coding RNA; DATABASES; GENOMES; NUCLEOTIDE sequencing
- Publication
Nature Communications, 2023, Vol 14, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-023-38785-y