rmMultiPCRChimera {CrispRVariants}R Documentation

Remove chimeric reads overlapping multiple primers

Description

Finds and removes sets of chimeric read alignments that overlap more than one guide, i.e. that cannot be unambiguously assigned to a single guide.

Usage

rmMultiPCRChimera(readnames, pcrhits, chimera_idxs, ...)

## S4 method for signature 'character,Hits,integer'
rmMultiPCRChimera(readnames, pcrhits,
  chimera_idxs, ..., verbose = TRUE)

Arguments

readnames

A set of read names, used for identifying chimeric read sets

pcrhits

A mapping between indices of reads and a set of pcr primers

chimera_idxs

location of chimeric reads within the bam

...

Additional arguments

verbose

Display information about the chimeras (Default: TRUE)

Value

pcrhits, with chimeric reads mapping to different primers omitted.

Author(s)

Helen Lindsay


[Package CrispRVariants version 1.8.0 Index]