qualityFiltering {genBaRcode}

Quality Filtering

Description

Excludes all sequences of a given fastq file below a certain quality value.

Usage

qualityFiltering(file_name, source_dir, min_score = 30)

Arguments

file_name

a character string containing the name of the source file.

source_dir

a character string containing the path to the source directory.

min_score

an integer value representing the minimal average phred score a read has to achieve in order to be accepted.

Value

a ShortRead object.

Examples

## Not run: 
source_dir <- system.file("extdata", package = "genBaRcode")
qualityFiltering(file_name = "test_data.fastq.gz", source_dir,
results_dir = getwd(), min_score = 30)

## End(Not run)