chimera (version 1.14.0)

tophatRun: 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 tophat is installed and located in the path. To run TopHat a softlink to bowtie or bowtie2 need to located in the user bin dir

Usage

tophatRun(input1, input2, output,cores=1, bowtie= c("bowtie","bowtie2"), tophat= "tophat",ebwt=paste(getwd(),"mychimera.fa",sep="/"),alignment=c("se","pe"))

Arguments

input1

The R1 fastq of a pair-end

input2

The R2 fastq of a pair-end

output

Folder in which tophat will generate the output

cores

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

bowtie

selecting bowtie or bowtie2 aligner

tophat

full path of tophat

ebwt

full path and name of the fasta file of one of the set of fusions of interest, to be used to build the bowtie 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

Value

TopHat standard output. The bam file of interest is accepted_hits.bam. The bam file will be then loaded in the slot fusionsLoc of the fSetSummary object from which fusions were retrieved.

See Also

chimeraSeqs

Examples

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