subreadRun: A function to generate a bam file for fusions coverage...
In chimera: A package for secondary analysis of fusion products

Description Usage Arguments Value Author(s) See Also Examples

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.

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

`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

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

Raffaele A Calogero

chimeraSeqs

   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)
   }