bam2fastq {chimera} | R Documentation

## A function to extract pair end reads from the bam file generated with subreadRun function

### Description

A function to extract pair end reads from the bam file generated with subread function. The output files are ready to be used for fusion validation with gapfiller

### Usage

    bam2fastq(bam, filename="ready4gapfiller",ref,parallel=FALSE)

### Arguments

`bam` | name of the bam file to be used for PE reads extraction
`filename` | base name for the PE fastq output data
`ref` | name of the fusion sequence that was used as reference
`parallel` | option that allow the use of BioParallel package

### Value

PE fastq files

### Author(s)

Raffaele A Calogero

### Examples

    #if(require(Rsubread)){
    # 	subreadRun(ebwt=paste(find.package(package="chimera"),"/examples/SULF2_ARFGEF2.fa",sep=""),
    #    input1=paste(find.package(package="chimera"),"/examples/mcf7_sample_1.fq",sep=""),
    #    input2=paste(find.package(package="chimera"),"/examples/mcf7_sample_2.fq",sep=""),
    #    outfile.prefix="accepted_hits", alignment="se", cores=1)
    #   ref.name <- names(readDNAStringSet(paste(find.package(package="chimera"),"/examples/SULF2_ARFGEF2.fa",sep=""), format="fasta"))
    #	bam2fastq(bam="accepted_hits.bam", filename="ready4gapfiller", ref=ref.name, parallel=F)
    #}

[Package chimera version 1.22.0 Index]