chimera (version 1.14.0)

gapfillerRun: A function to confirm fusion break point by de novo assembly

Description

A function that uses GapFiller to confirm, by de novo assembly, the presence of the fusion break point. The function needs as input the fusion transcript generated by chimeraSeqs function and two fastq files corresponding to the reads mapping over the fusion transcript.

Usage

gapfillerRun(fusion.fa, seed1,  seed2, gapfiller=NULL, seed.ins=200, seed.var=50, 
block.length=5, overlap=20, max.length=5000, slack=30, 
k=6, global.mismatch=5)

Arguments

fusion.fa

fasta file with the fusin transcript

seed1

The R1 fastq of a pair-end

seed2

The R2 fastq of a pair-end

gapfiller

path to GapFiller executable program

seed.ins

seed reads insert size

seed.var

seed reads insert variation

block.length

length of perfect match

overlap

minimum suffix-prefix overlap

max.length

print only contigs

slack

number of overlaps: suffix-prefix overlap range is given by overlap, overlap + slack

k

length of the word used to hash

global.mismatch

maximum number of mismatches between mate and contig

Value

The program will write in a temporary directory contigs.fasta and contig.stats, which are used to evaluate if the de novo assembly allows the identification of the fusion break point. The function returns a list of three objects. The list is returned only in case that some of de novo assemblies cover the breakpoint junction. The list is made of:

contigs

which is a PairwiseAlignments object

junction.contigs

which is a DNAStringSet encompassing the sequences present in the contigs object

fusion

which is a DNAStringSet object encompassing the fusion transcript

See Also

chimeraSeqs, gapfillerInstallation

Examples

#	tmp <- gapfillerRun(fusion.fa=paste(path.package("chimera", quiet = FALSE),"/examples/uc002xvp.1-243_uc002iyu.4-1031.fa",sep=""),seed1=paste(path.package("chimera", quiet = FALSE),"/examples/uc002xvp.1-243_uc002iyu.4-1031_R1.fastq",sep=""),  seed2=paste(path.package("chimera", quiet = FALSE),"/examples/uc002xvp.1-243_uc002iyu.4-1031_R1.fastq",sep=""))