fastqPatternSearch | R Documentation |
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.
matchPattern
, in the Biostrings package.
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