qualityFiltering: Quality Filtering
In genBaRcode: Analysis and Visualization Tools for Genetic Barcode Data

qualityFiltering

R Documentation

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)

genBaRcode documentation built on March 31, 2023, 11:02 p.m.