readsByPCRPrimer: Finds overlaps between aligned reads and PCR primers

In CrispRVariants: Tools for counting and visualising mutations in a target location

Description

Short reads amplified with PCR primers should start and end at defined positions. However, the ends of an aligned read may be clipped as sequencing technologies are prone to making errors at the start and end. readsByPCRPrimer extrapolates the genomic location of entire reads from their aligned sections by adding clipped sections, then finds near exact matches to a set of PCR primers. Note that this is not always a good assumption, and is misleading in the case of chimeric reads where sections clipped in one part of a chimera are aligned in another.

Usage

readsByPCRPrimer(bam, primers, ...)

## S4 method for signature 'GAlignments,GRanges'
readsByPCRPrimer(bam, primers, ...,
  tolerance = 0, verbose = TRUE, ignore.strand = TRUE,
  allow.partial = TRUE, chimera.idxs = NULL)

## S4 method for signature 'GRanges,GRanges'
readsByPCRPrimer(bam, primers, ..., tolerance = 0,
  verbose = TRUE, ignore.strand = TRUE, allow.partial = TRUE,
  chimera.idxs = NULL)

Arguments

bam	A set of aligned reads
primers	A set of ranges that the unclipped reads may map to
...	Additional arguments
tolerance	Number of bases by which reads and primers may differ at each end (Default: 0)
verbose	Print number of full and partial matches (Default: TRUE)
ignore.strand	Passed to findOverlaps and disjoin. Should strand be ignored when finding overlaps. (Default: TRUE)
allow.partial	Should reads that do not match the PCR boundaries, but map to a region covered by only one primer be considered matches? (Default: TRUE)
chimera.idxs	Indices of chimeric reads within the bam. If specified, chimeras overlapping multiple pcr primers will be removed.

Value

A Hits object where "query" is the index with respect to bam and "subject" is the index with respect to the primers.

Author(s)

Helen Lindsay

See Also

GRanges, GAlignments

CrispRVariants documentation built on Nov. 8, 2020, 11:09 p.m.