seqTools (version 1.6.0)

fastqKmerLocs: fastqKmerLocs function: Counts DNA k-mers position wise from FASTQ files.

Description

Reads (compressed) FASTQ files and counts for DNA k-mers for each position in sequence.

Usage

fastqKmerLocs(filenames, k=4)

Arguments

filenames

Vector of FASTQ file names. Files can be gz compressed.

k

Length of counted DNA k-mers.

Value

. The length of the list equals the number of given filenames. Contains for each given file a matrix with 4^k rows and (maxSeqLen - k + 1) columns (maxSeqLen= maximum read length). The matrix contains for each k-mer and k-mer-start position the counted values.

Details

Maximal allowed value for k is 12.

References

Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM The sanger FASTQ file format for sequences with quality scores and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2010 Vol.38 No.6 1767-1771

Examples

basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2)
res <- fastqKmerLocs("test_l10_atcg.fq", k=2)
res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2)
res <- fastqKmerLocs("test_l6_multi_line.fq", k=2)