OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data

Abstract

Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by biologists, we developed a web application called OneStopRNAseq for the one-stop analysis of RNA-seq data. OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. Users only need to select the desired analyses and genome build, and provide a Gene Expression Omnibus (GEO) accession number or Dropbox links to sequence files, alignment files, gene-expression-count tables, or rank files with the corresponding metadata. Our pipeline facilitates the comprehensive and efficient analysis of private and public RNA-seq data.

RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow

“…A graphical user interface comes with [ 6 ] provided within the Galaxy framework [ 52 ]. [ 53 ] offers a web application that requires a login for full usage. The back-end is implemented within the Snakemake framework.…”

“…✓—feature available/supported; ✗—feature not available/supported; ✱—feature partially supported. RNAflow VIPER [ 4 ] Nextpresso [ 5 ] TRAPLINE [ 6 ] RNAsik [ 7 ] hppRNA [ 8 ] nf-core/rnaseq [ 9 ] RCP [ 10 ] RASflow [ 50 ] OneStopRNAseq [ 53 ] Pipeline scope Read QC ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ Trimming ✓ ✗ ✓ ✓ ✗ ✓ ✓ ✓ ✓ ✗ rRNA removal ✓ ✱ no automatic removal ✗ ✗ ✗ ...…”

Aryl hydrocarbon receptor and TGF-β inducible early gene mediate a transcriptional axis modulating immune homeostasis in mosquitoes

“…gambiae (NCBI), implemented by using Array Star v.12 (DNAstar). Read counts were normalized using the median of ratios method [26] using DESeq2 software [27]. In determining normalized read counts, this method accounts for sequencing depth and RNA composition by calculating normalization factors for each sample in comparison to a pseudo-reference sample.…”

“…Likelihood ratio tests were conducted to identify transcripts that exhibited differential expression between all groups. Pairwise differential expression comparisons were made and statistical significance was determined by computing q-values that preserve the False Discovery Rate (FDR) [28, 29] [26]. For example, concluding that a transcript was differentially expressed between two groups with a q-value of 0.05 would imply that there was a 5% chance (expected) that this conclusion was a false positive.…”

Emerging Trends in Deciphering the Pathogenesis of Human Diseases through Genetic Analysis

“…Although many RNA sequencing (RNA-seq) data have been deposited in public repositories, there are few open source tools with point-and-click interfaces that are versatile and offer a streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by researchers and scientists, Li et al developed a new Web application called OneStopRNAseq for the one-stop analysis of RNA-seq data [ 3 ]. The pipeline has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, which can greatly facilitate the comprehensive and efficient analysis of private and public RNA-seq data.…”