pairUpAlignments: Pair up alignments in a GRanges object

In malnirav/hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description

Given a GRanges object, the function uses specified gaplength parameter to pair up reads where the qName column ends with "atpersand pairname atpersand" which is outputted by extractSeqs.

Usage

pairUpAlignments(
  psl.rd = NULL,
  maxGapLength = 2500,
  sameStrand = TRUE,
  parallel = TRUE
)

Arguments

psl.rd	a GRanges object with qNames ending in "atpersand pairname atpersand".
maxGapLength	maximum gap allowed between end of pair1 and start of pair2. Default is 2500 bp.
sameStrand	should pairs be aligned to the same strand or in same orientationin the reference genome? Default is TRUE. This is 'TRUE' because pair2 reads are reverseComplemented when reading in data in findBarcodes
parallel	use parallel backend to perform calculation with BiocParallel. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using SerialParam.

Value

a GRanges object with reads paired up denoted by "paired" column. Improper pairs or unpaired reads are returned with "paired" column as FALSE.

See Also

pairwiseAlignSeqs, blatSeqs, read.blast8, read.psl, getIntegrationSites, read.BAMasPSL

Examples

 
## Not run: 
psl.rd <- read.BAMasPSL(bamFile=c("sample1hits.bam","sample2hits.bam"))
pairUpAlignments(psl.rd)

## End(Not run)

malnirav/hiReadsProcessor documentation built on July 29, 2021, 6:33 a.m.