trumpet: transcriptome-guided quality assessment of m(6)A-seq data

BACKGROUND: Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m(6)A-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, m(6)A-seq data often suffer from various flaws. A convenient and comprehensive tool is needed to assess the quality of m(6)A-seq data to ensure that they are suitable for subsequent analysis. RESULTS: From a technical perspective, m(6)A-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 m(6)A-seq data quality. The trumpet package takes the aligned BAM files from m(6)A-seq data together with the transcriptome information as the inputs to generate a quality assessment report in the HTML format. CONCLUSIONS: The trumpet R package makes a valuable tool for assessing the data quality of m(6)A-seq, and it is also applicable to other fragmented RNA immunoprecipitation sequencing techniques, including m(1)A-seq, CeU-Seq, Ψ-seq, etc. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2266-3) contains supplementary material, which is available to authorized users.