trimFastq: trimFastq: Performs sequence removal, trimming (fixed and...
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files

Description Usage Arguments Details Value Author(s) References Examples

Fastq files sometimes need to be preprocessed before alignment. Three different mechanisms come into use here: Discarding whole reads, trimming sequences and masking nucleotides. This function performs all three mechanisms together in one step. All reads with insufficient phred are discarded. The reads can be trimmed ad each terminal side (on trim of fixed size and a trim based on quality thresholds).

trimFastq(infile, outfile="keep.fq.gz", discard="disc.fq.gz",
        qualDiscard=0, qualMask=0, fixTrimLeft=0,
        fixTrimRight=0, qualTrimLeft=0, qualTrimRight=0,
        qualMaskValue=78, minSeqLen=0)

infile

character. Input FASTQ file. Only one infile is allowed per function call.

outfile

character. Output FASTQ file.

discard

character. Output file in which discarded reads are written.

qualDiscard

numeric. All reads which contain one or more phred scores <qualDiscard will be discarded (i.e. output to discard).

qualMask

numeric. All nucleotides for which phred score < qualMask will be overwritten with qualMaskValue.

fixTrimLeft

numeric. Prefix of this size will be trimmed.

fixTrimRight

numeric. Suffix of this size will be trimmed.

qualMaskValue

numeric. ASCII replace value for masked nucleotides

qualTrimLeft

numeric. Prefix where all phred scores are < qualTrimLeft will be trimmed.

qualTrimRight

numeric. Suffix where all phred scores are < qualTrimRight will be trimmed.

minSeqLen

numeric. All reads where sequence length after (fixed and quality based) trimming is <minSeqLen will be descarded (i.e. output to discard).

The function divides the input file into two outputs: The output file (contains the accepted reads) and the discard file (contains the excluded reads). After trim operations, the function checks for remaining read length. When the read length is smaller than minSeqLen, the read will be discarded.

Numeric. A vector of length 2 which contains the number of reads which are written to output and to discard

Wolfgang Kaisers

Ewing B, Green P Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 1998 Vol. 8 No. 3 186-194

basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
trimFastq("sim.fq.gz", qualDiscard=10, qualMask=15, fixTrimLeft=2,
    fixTrimRight=2, qualTrimLeft=28, qualTrimRight=30, minSeqLen=5)