SRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

Ernesto Aparicio-Puerta,Antonio Rueda,Cristina Gómez-Martín,David Jaspez,José Oliver,Igor Jurak,Ricardo Lebrón,Juan Antonio Marchal,Michael Hackenberg,José María Medina,Stavros Giannoukakos,Bastian Fromm,Andreja Zubkovic

doi:10.1093/nar/gkz415

Abstract

Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well as microRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNA-seq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.

Highlights

Small RNA profiling by means of miRNA-seq is a key step in many study designs because it often precedes further downstream analysis such as screening, prediction, identification and validation of miRNA targets or biomarker detection [1,2]
In 2015, we introduced sRNAtoolbox [9], a collection of small RNA research tools built around sRNAbench, providing different downstream analysis including consensus differential expression, target prediction and analysis of unmapped reads by means of blast searches against general nucleotide databases
The increase in sequencing volume has been accompanied by the publication of new library preparation protocols, each of which involves specific pre-processing steps in the bioinformatics analysis

Summary

Introduction

Small RNA profiling by means of miRNA-seq (or small RNA-seq) is a key step in many study designs because it often precedes further downstream analysis such as screening, prediction, identification and validation of miRNA targets or biomarker detection [1,2]. In 2015, we introduced sRNAtoolbox [9], a collection of small RNA research tools built around sRNAbench, providing different downstream analysis including consensus differential expression, target prediction and analysis of unmapped reads by means of blast searches against general nucleotide databases.

Results

Conclusion