find_format: Gets quality score encoding format from the FASTQ file....

In compbiocore/qckitfastq: FASTQ Quality Control

Description

Gets quality score encoding format from the FASTQ file. Return possibilities are Sanger(/Illumina1.8), Solexa(/Illumina1.0), Illumina1.3, and Illumina1.5. This encoding is heuristic based and may not be 100 since there is overlap in the encodings used, so it is best if you already know the format.

Usage

find_format(infile, reads_used)

Arguments

infile	A string giving the path for the fastq file
reads_used	int, the number of reads to use to determine the encoding format.

Value

A string denoting the read format. Possibilities are Sanger, Solexa, Illumina1.3, and Illumina1.5.

Examples

infile <- system.file("extdata", "10^5_reads_test.fq.gz", package = "qckitfastq")
find_format(infile,100)

compbiocore/qckitfastq documentation built on Sept. 20, 2019, 9:30 a.m.