bam2fastq: A function to extract pair end reads from the bam file...
In chimera: A package for secondary analysis of fusion products

Description Usage Arguments Value Author(s) Examples

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

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

`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

PE fastq files

Raffaele A Calogero

#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)
#}