bam2fastq {chimera} | R Documentation |
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
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) #}