Trumpet: transcriptome-guided quality assessment of m⁶A-seq data.

ABSTRACT:

Background

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.

Results

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.

Conclusions

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.

SUBMITTER: Zhang T 

PROVIDER: S-EPMC6044007 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature