chimera (version 1.14.0)

starRun: 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 assumes that STAR is installed and located in the path.

Usage

starRun(input1, input2, cores=1, star= "STAR", samtools="samtools", fa, alignment=c("se","pe"), chimSegmentMin=0, chimJunctionOverhangMin=20)

Arguments

input1

The R1 fastq of a pair-end

input2

The R2 fastq of a pair-end

cores

number of cores to be used by tophat with program name, e.g. /somewhere/tophat

star

full path of STAR with program name, e.g. /somewhere/STAR

samtools

full path of samtools

fa

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

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

chimSegmentMin

STAR fusion parameter, see STAR manual

chimJunctionOverhangMin

STAR fusion parameter, see STAR manual

Value

The function create a folder called chimeraDB_time, where time is the time when the folder was created. STAR output will be located in the folder output_time, where time is the time when the folder was created. The bam file of interest is accepted_hits.bam.

See Also

chimeraSeqs

Examples

#starRun(input1=paste(find.package(package="chimera"),"/examples/mcf7_sample_1.fq",sep=""), input2=paste(find.package(package="chimera"),"/examples/mcf7_sample_2.fq",sep=""), fa=paste(find.package(package="chimera"),"/examples/SULF2_ARFGEF2.fa",sep=""), alignment="se", output=getwd(), cores=1)