Trumpet: an R package for transcriptome-guided quality assessment of m6A-seq data

Motivation: Methylated RNA immunoprecipitation sequencing (m6A-seq or MeRIP-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-MethylAdenosine methylation. However, due to the intrinsic properties of RNA molecule and the intricate procedures of this technique, m6A-seq data often suffers from various flaws. A convenient and comprehensive tool is solely needed to assess the quality of m6A-seq data to ensure it is suitable for subsequent analysis.

Results: From a technical perspective, m6A-seq can be considered as a marriage 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. Trumpet package takes the aligned BAM files from m6A-seq data together with transcriptome information as inputs to generate a quality assessment report in HTML format.

Installation Instructions

The Trumpet package can be installed by the following R commands:

devtools::install_github("skyhorsetomoon/Trumpet")

library(Trumpet)

Usage Example

The following command code will show how to use this package and generate the assessment report in HTML format.

Input the samples to be evaluated in BAM files and generate the assessment report directly.

Collect the path of all the aligned MeRIP-seq data files in BAM format.

f1 <- system.file("extdata", "IP1.bam", package="Trumpet")

f2 <- system.file("extdata", "IP2.bam", package="Trumpet")

f3 <- system.file("extdata", "IP3.bam", package="Trumpet")

f4 <- system.file("extdata", "IP4.bam", package="Trumpet")

f5 <- system.file("extdata", "Input1.bam", package="Trumpet")

f6 <- system.file("extdata", "Input2.bam", package="Trumpet")

f7 <- system.file("extdata", "Input3.bam", package="Trumpet")

f8 <- system.file("extdata", "treated_IP1.bam", package="Trumpet")

f9 <- system.file("extdata", "treated_Input1.bam", package="Trumpet")

ip_bam <- c(f1,f2,f3,f4)

input_bam <- c(f5,f6,f7)

contrast_ip_bam <- c(f8)

contrast_input_bam <- c(f9)

We use GTF file in the following example.

gtf <- system.file("extdata", "hg19toy.gtf", package="Trumpet")

We can call the main function to generate the assessment report under current working directory.

trumpet_report <- Trumpet_report(IP_BAM = ip_bam, Input_BAM = input_bam, contrast_IP_BAM = contrast_ip_bam, contrast_Input_BAM = contrast_input_bam, condition1 = "untreated", condition2 = "treat, GENE_ANNO_GTF = gtf)

It can be opened with a web browser or with the following R command.

browseURL("Trumpet_report.html")