Description Usage Arguments Details Value Author(s)
Calculate percentages of nucleotides A, T, G and C in the input FASTQ or FASTQ file.
1 2 3 4 | atgcContent(
filename,
basewise = FALSE)
|
filename |
a character string giving the name of input FASTQ/FASTA file |
basewise |
logical specifying how the percentages are calculated. If |
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.
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.
Zhiyin Dai and Wei Shi
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