chimera (version 1.14.0)

bam2fastq: 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

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)
#}