Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework

Niko Popitsch; Tobias Neumann; Arndt von Haeseler; Stefan L. Ameres

doi:10.1186/s13059-024-03313-8

Titel

Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework

Autor*in

Niko Popitsch

Department für Biochemie und Zellbiologie, Max Perutz Labs, Universität Wien

Tobias Neumann

Max Perutz Labs, Universität Wien

Arndt von Haeseler

Forschungsgruppe Bioinformatics and Computational Biology, Fakultät für Informatik, Universität Wien

... show all

Abstract

Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases in mapping the resulting reads to reference genomes remain poorly understood. We present splice_sim, a splice-aware RNA-seq simulation and evaluation pipeline that introduces user-defined nucleotide conversions at set frequencies, creates mixture models of converted and unconverted reads, and calculates mapping accuracies per genomic annotation. By simulating nucleotide conversion RNA-seq datasets under realistic experimental conditions, including metabolic RNA labeling and RNA bisulfite sequencing, we measure mapping accuracies of state-of-the-art spliced-read mappers for mouse and human transcripts and derive strategies to prevent biases in the data interpretation.

Stichwort

Nucleotide conversion sequencingMetabolic RNA labelingSLAMseqRNA-BS-seq3′ end sequencingSpliced read mappingRead mapping accuracy

Objekt-Typ

journal article

Sprache

Englisch [eng]

Persistent identifier

phaidra.univie.ac.at/o:2076355

DOI

10.1186/s13059-024-03313-8

Erschienen in

Titel