Comparison of alternative approaches for analysing multi-level RNA-seq data

RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D. melanogaster that was used here.

University of East Anglia researchers investigated the power of existing approaches for quality checking mRNA-seq data and explored additional, quantitative quality checks. To accommodate nested, multi-level experimental designs, they incorporated sample layout into our analyses. They employed a subsampling without replacement-based normalization and an identification of DE that accounted for the hierarchy and amplitude of effect sizes within samples, then evaluated the resulting differential expression call in comparison to existing approaches. In a final step to test for broader applicability, the researchers applied their approaches to a published set of H. sapiens mRNA-seq samples, The dataset-tailored methods improved sample comparability and delivered a robust prediction of subtle gene expression changes. The proposed approaches have the potential to improve key steps in the analysis of RNA-seq data by incorporating the structure and characteristics of biological experiments.

Analysis framework for the D. melanogaster mRNA-seq data


Required inputs (sequencing data in FASTQ format, the corresponding reference genome and transcriptome in FASTA/GFF) and the six main steps of the analysis are shown in a workflow diagram, following Conesa et al. 2016 (Genome Biology, 17:13). The steps, for which additional details are included, are: Quality check (QC), alignment, normalization of gene abundances, identification of DE, functional enrichment and finally low-throughput validation.

Mohorianu I, Bretman A, Smith DT, Fowler EK, Dalmay T, Chapman T (2017) Comparison of alternative approaches for analysing multi-level RNA-seq data. PLoS ONE 12(8): e0182694. [article]

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