chimera (version 1.14.0)

subreadRun: A function to generate a bam file for fusions coverage evaluation

Description

A function mapping reads to a chimera sequence set. The bam produced by this remapping on a putative fusion will be used to plot the coverage data for all the fused constructs. The function uses Rsubread aligner for MAC and UNIX OS. In case WINDOWS OS Rbowtie is used.

Usage

subreadRun(ebwt,input1, input2, outfile.prefix="accepted_hits", alignment=c("se","pe"),cores=1)

Arguments

ebwt

Full path and name of the fasta file of one of the set of fusions of interest, to be used to build the index database. The fusion nucleotide sequences can be generated with the function chimeraSeqs

input1

The R1 fastq of a pair-end

input2

The R2 fastq of a pair-end

outfile.prefix

Prefix of the output bam file. Default is accepted_hits

alignment

se means that both fastq files from the pair-end run are concatenated, pe means that tophat will use fastq files in pair-end mode

cores

Number of cores to be used by the aligner

Value

Standard bam file output. The bam file name by default is accepted_hits.bam.

See Also

chimeraSeqs

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)
   }