trumpet: transcriptome-guided quality assessment of m<SUP>6</SUP>A-seq data

Zhang, Teng, Zhang, Shao-Wu, Zhang, Lin and Meng, Jia ORCID: 0000-0003-3455-205X (2018) trumpet: transcriptome-guided quality assessment of m<SUP>6</SUP>A-seq data. BMC BIOINFORMATICS, 19 (1). 260-.

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Abstract

<h4>Background</h4>Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m⁶A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic properties of RNA molecules and the intricate procedures of this technique, m⁶A-seq data often suffer from various flaws. A convenient and comprehensive tool is needed to assess the quality of m⁶A-seq data to ensure that they are suitable for subsequent analysis.<h4>Results</h4>From a technical perspective, m⁶A-seq can be considered as a combination of ChIP-seq and RNA-seq; hence, by effectively combing the data quality assessment metrics of the two techniques, we developed the trumpet R package for evaluation of m⁶A-seq data quality. The trumpet package takes the aligned BAM files from m⁶A-seq data together with the transcriptome information as the inputs to generate a quality assessment report in the HTML format.<h4>Conclusions</h4>The trumpet R package makes a valuable tool for assessing the data quality of m⁶A-seq, and it is also applicable to other fragmented RNA immunoprecipitation sequencing techniques, including m¹A-seq, CeU-Seq, Ψ-seq, etc.

Item Type:	Article
Uncontrolled Keywords:	m(6)A-seq, RNA methylation, Data quality, Assessment metrics, trumpet R package
Depositing User:	Symplectic Admin
Date Deposited:	14 Mar 2019 15:38
Last Modified:	15 Oct 2023 01:31
DOI:	10.1186/s12859-018-2266-3
Open Access URL:	https://doi.org/10.1186/s12859-018-2266-3
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3034273