trumpet

trumpet assesses the quality of methylated RNA immunoprecipitation sequencing (MeRIP-seq) data, focusing on N6-Methyladenosine (m^6A) methylation profiling.

Key Features:

• R package: Implemented as an R package for analysis of MeRIP-seq data.
• Target modification: Focuses on N6-Methyladenosine (m^6A) profiling from MeRIP-seq (m^6A-seq) experiments.
• Hybrid QC metrics: Integrates quality assessment metrics from both ChIP-seq and RNA-seq methodologies to reflect MeRIP-seq's hybrid nature.
• Input requirements: Accepts aligned BAM files generated from m^6A-seq experiments and transcriptome information.
• Output: Generates an HTML-formatted quality assessment report.
• Applicability: Applicable to other fragmented RNA immunoprecipitation sequencing techniques including N1-Methyladenosine (m^1A-seq), Cytidine-to-Uridine editing sequencing (CeU-Seq), and Pseudouridine sequencing (Ψ-seq).

Scientific Applications:

• m^6A-seq quality assessment: Evaluating integrity and suitability of m^6A-seq datasets for downstream analyses.
• RNA modification IP-seq QC: Performing quality control on m^1A-seq, CeU-Seq, and Ψ-seq datasets.
• Technical evaluation: Assessing the technical characteristics of MeRIP-seq by combining ChIP-seq and RNA-seq quality metrics.

Methodology:

Integrates quality assessment metrics from ChIP-seq and RNA-seq methodologies using aligned BAM files and transcriptome information as input and produces an HTML-formatted quality assessment report.