chimera (version 1.14.0)

gapfillerWrap: A function to prepare files and to run gapfiller

Description

A function that uses GapFiller to confirm, by de novo assembly, the presence of the fusion break point. The function needs as input a list of fusion transcript generated by chimeraSeqSet function and the bam file containing the reads remapped over the fusion transcripts made using subreadRun.

Usage

gapfillerWrap(chimeraSeqSet.out, bam, parallel=c(FALSE,TRUE))

Arguments

chimeraSeqSet.out

a list of DNAStringSet output from chimeraSeqSet

bam

bam file containing the reads remapped over the fusion transcripts using Rsubread

parallel

if FALSE FALSE no parallelization, if TRUE TRUE full paralleization, if FALSE TRUE only parallelization for internal funtions

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 for each fusion 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, gapfillerRun

Examples

#tmp <- importFusionData("star", "Chimeric.out.junction", org="hg19", min.support=100)
#myset <- tmp[1:4]
#tmp.seq <- chimeraSeqsSet(myset, type="transcripts")
#tmp <- gapfillerWrap(chimeraSeqSet.out=trsx, bam="accepted_hits_mapped.bam", parallel=c(FALSE,TRUE))