Rsubread (version 1.22.2)

atgcContent: Calculate percentages of nucletodies A, T, G and C in a sequencing read datafile

Description

Calculate percentages of nucletodies A, T, G and C

Usage

atgcContent(filename, basewise=FALSE)

Arguments

filename

character string giving the name of input FASTQ/FASTA file

basewise

logical. 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.

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.

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.