sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression
Metadatos
Mostrar el registro completo del ítemAutor
Aparicio Puerta, Ernesto; Lebrón Aguilar, Ricardo; Rueda, Antonio; Gómez Martín, Cristina; Giannoukakos, Stavros Panagiotis; Jaspez, David; Medina Casaubón, José María; Zubkovic, Andreja; Jurak, Igor; Fromm, Bastian; Marchal Corrales, Juan Antonio; Oliver Jiménez, José Lutgardo; Hackenberg, MichaelEditorial
Oxford University Press
Fecha
2019-05-22Referencia bibliográfica
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.
Patrocinador
European 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].Resumen
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.