seqTools-package {seqTools} | R Documentation |
Analyze read length, phred scores and alphabeth frequency and DNA k-mers on uncompressed and compressed files.
Package: | seqTools |
Type: | Package |
Version: | 0.99.31 |
Date: | 2013-10-14 |
License: | GPL-2 |
Depends: | methods |
Wolfgang Kaisers Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
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
# A) Count DNA k-mer countDnaKmers("ATAAATA", 2) # B) Quality check on FASTQ file basedir <- system.file("extdata", package="seqTools") setwd(basedir) fq <- fastqq("test_l6.fq") plotPhredQuant(fq, 1)