fastqPatternSearch: Find DNA Patterns in FASTQ Reads
In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

fastqPatternSearch

R Documentation

Find DNA Patterns in FASTQ Reads

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

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

`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

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

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