fastqPatternSearch: Find DNA Patterns in FASTQ Reads

Description Usage Arguments Details Value See Also

Description

Find and count the frequency of DNA patterns in the reads of a FASTQ file

Usage

1
fastqPatternSearch(filein, patterns, max.mismatch = 0, chunkSize = 4e+05)

Arguments

filein

name of existing FASTQ file to search

patterns

character vector of DNA nucleotide patterns to search for

max.mismatch

maximum number of mismatching nucleotides allowed in a 'match'

chunkSize

buffer size, in number of reads

Details

Uses the Biostrings package. Useful for counting the number of reads containing a known DNA sequence, such as adapter end primers.

Value

numeric vector of length length(patterns), giving the number of reads that contain each pattern.

See Also

matchPattern, in the Biostrings package.


robertdouglasmorrison/DuffyTools documentation built on Dec. 14, 2018, 3:05 p.m.