trimAdapter: Remove 3' adapter contamination
In girafe: Genome Intervals and Read Alignments for Functional Exploration

Description Usage Arguments Details Value Note Author(s) See Also Examples

Function to remove 3' adapter contamination from reads

1 2	trimAdapter(fq, adapter, match.score = 1, mismatch.score = -1, score.threshold = 2)

`fq`	Object of class `ShortReadQ`; the reads with possible adapter contamination.
`adapter`	object of class `DNAString` or class `character`; the sequence of the 3' adapter which could give rise to the 3' contamination. If of class `character`, it is converted to a `DNAString` inside the function.
`match.score`	numeric; alignment score for matching bases
`mismatch.score`	numeric; alignment score for mismatches
`score.threshold`	numeric; minimum total alignment score required for an overlap match between the 3' end of the read and the 5' end of the adapter sequence.

Performs an overlap alignment between the ends of the reads and the start of the adapter sequence.

An object of class ShortReadQ containing the reads without the 3' adapter contamination.

The function trimLRPatterns from package ShortRead may be a faster alternative to this function.

J. Toedling

pairwiseAlignment, narrow, readFastq, writeFastq

  exDir <- system.file("extdata", package="girafe")
  ## load reads containing adapter fragments at the end
  ra23.wa  <- readFastq(dirPath=exDir, pattern=
              "aravinSRNA_23_plus_adapter_excerpt.fastq")
  table(width(ra23.wa))
  # adapter sequence obtained from GEO page
  #  accession number: GSE10364
  #adapter <- DNAString("CTGTAGGCACCATCAAT")
  adapter <- "CTGTAGGCACCATCAAT"

  # trim adapter
  ra23.na  <- trimAdapter(ra23.wa, adapter)
  table(width(ra23.na))