RNA Editing Detection in HPC Infrastructures.

Autor: Lo Giudice C; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy., Mansi L; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy., Flati T; SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy., Gioiosa S; SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy., Chillemi G; SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy.; Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Viterbo, Italy., Libro P; Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy., Castrignanò T; Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy., Pesole G; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.; Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy.; National Institute of Biostructures and Biosystems (INBB), Rome, Italy., Picardi E; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy. ernesto.picardi@uniba.it.; Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy. ernesto.picardi@uniba.it.; National Institute of Biostructures and Biosystems (INBB), Rome, Italy. ernesto.picardi@uniba.it.
Jazyk: angličtina
Zdroj: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2284, pp. 253-270.
DOI: 10.1007/978-1-0716-1307-8_14
Abstrakt: RNA editing by A-to-I deamination is a relevant co/posttranscriptional modification carried out by ADAR enzymes. In humans, it has pivotal cellular effects and its deregulation has been linked to a variety of human disorders including neurological and neurodegenerative diseases and cancer. Despite its biological relevance, the detection of RNA editing variants in large transcriptome sequencing experiments (RNAseq) is yet a challenging computational task. To drastically reduce computing times we have developed a novel REDItools version able to identify A-to-I events in huge amount of RNAseq data employing High Performance Computing (HPC) infrastructures.Here we show how to use REDItools v2 in HPC systems.
Databáze: MEDLINE
Externí odkaz: