sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression
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AuthorAparicio Puerta, Ernesto; Lebrón, Ricardo; Rueda, Antonio; Gómez Martín, Cristina; Giannoukakos, Stavros; Jaspez, David; Medina Casaubón, José María; Zubkovic, Andreja; Jurak, Igor; Fromm, Bastian; Marchal Corrales, Juan Antonio; Oliver Jiménez, José Lutgardo; Hackenberg, Michael
Oxford University Press
Aparicio-Puerta, E., Lebrón, R., Rueda, A., Gómez-Martín, C., Giannoukakos, S., Jaspez, D., ... & Marchal, J. A. (2019). sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression. Nucleic acids research, 47(W1), W530-W535.
SponsorshipEuropean Union [765492 to M.H.]; Spanish Government [AGL2017-88702-C2-2-R to M.H., J.L.O.]; Instituto de Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.]; Chair ‘Doctors Galera-Requena in cancer stem cell research’ to JMA and by the Ministry of Education of Spain [FPU13/05662 to R.L., IFI16/00041 to E.A.]; Strategic Research Area (SFO) program of the Swedish Research Council (to V.R.) through Stockholm University (to B.F.). Funding for open access charge: SpanishGovernment [AGL2017-88702-C2-2-R].
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 asmicroRNA 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 miRNAseq 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.