converting bam file to bed

Question

[azzopardiannalise]

Hi,

I am trying to convert a bam file to a bed file using R software however, I am currently unsuccessful. The below is what I have inputted so far in R-software can anyone help me please?

#load library
library(Rsamtools)
library(RNAseqData.HNRNPC.bam.chr14)
library(GenomicAlignments)
bamfile <- file.path("C:","Users","azzop","Desktop","I16-1144-01-esd_m1_CGCTCATT-AGGCGAAG_tophat2","accepted_hits.bam")

system(paste("bedtools bamtobed -i", bamfile, "> myBed.bed"))
library(data.table)
myData <- fread("myBed.bed")

Does anyone know how I can use the package bedtools in R? What am I doing is it correct?

Also, my goal is to combine more than 1 bam file together as I have 9 bam files and I would need to analyze the data holistically? Any suggestions?

Thanks, A

[WouterDeCoster]

The first question would be why you are trying to do this in R... Looks you are using windows, can you use the WSL/Ubuntu?

[azzopardiannalise]

Yes I am using windows as this is part of my dissertation for MSc in statistics and I will be using R stoftware to analyze the data

[WouterDeCoster]

If you are using Windows 10 I recommend WSL: the Windows Subsystem for Linux. That will make your work a lot easier.

R is a programming language. While you technically can execute bedtools through R you are then no longer using R itself. It's just a vehicle to execute bedtools and it adds an unnecessary layer of complexity.

Answer 1

[Alex Reynolds]

Via BEDOPS:

$ bam2bed < reads.bam > reads.bed