atgcContent {Rsubread} | R Documentation

## Calculate Percentages of Nucleotides in Reads

### Description

Calculate percentages of nucleotides A, T, G and C in the input FASTQ or FASTQ file.

### Usage

    atgcContent(

        filename,
        basewise = FALSE)

### Arguments

`filename` | a character string giving the name of input FASTQ/FASTA file
`basewise` | logical specifying how the percentages are calculated. If `TRUE`, nucleotide percentages will be calculated for each base position in the read across all the reads. By default, percentages are calculated for the entire dataset.

### Details

Sequencing reads could contain letter "N" besides "A", "T", "G" and "C". Percentage of "N" in the read dataset is calcuated as well.

The `basewise` calculation is useful for examining the GC bias towards the base position in the read. By default, the percentages of nucleotides in the entire dataset will be reported.

### Value

A named vector containing percentages for each nucleotide type if `basewise` is `FALSE`. Otherwise, a data matrix containing nucleotide percentages for each base position of the reads.

### Author(s)

Zhiyin Dai and Wei Shi

[Package Rsubread version 2.4.3 Index]