Question: Visualize nucleotides for every position in R
2
9 months ago by
marija30
Croatia
marija30 wrote:

Hi, please, how can I visualize nucelotides for every position. I have a percentage of bases but now I don't know how to create a plot.

``````fastq <- readDNAStringSet("https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/ERR037900_1.first1000.fastq","fastq")
fastq
freq <- alphabetFrequency(fastq, as.prob = T,baseOnly=T)
``````

I would like something like this (sorry for quality):

R • 492 views
modified 9 months ago by cpad01129.1k • written 9 months ago by marija30
1
4
9 months ago by
India

You need to change your code. It is not alphabet frequency. It is consensus matrix. Example code and image below:

``````library(Biostrings)
## At each position, base frequency
afmc=consensusMatrix(fastq, baseOnly=T,as.prob = T)
tafmc=t(afmc)
matplot(tafmc[,-5], type="l", lwd=2, xlab="Read Length", ylab= "Base frequency at each position")
legend(legend = colnames(tafmc)[-5],"topright",col=1:4, lty=1:4, lwd=2)
``````

5th column is others (other than A,T, G and C).

Awesome, thank you very much.

much simpler is using SeqTools in R:

``````library(seqTools)
# Reads fastq file
fq=fastqq("sample.fastq")
# Plots nucleotide frequency
plotNucFreq(fq,1)
``````

2
9 months ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:
``````library(Biostrings)
freq <- alphabetFrequency(fastq, as.prob = T,baseOnly=T)
matplot(freq,type='l')
legend(legend = colnames(freq),x=700,y=0.7,lty=1:5,col=1:5)
``````

Note answer about consensusMatrix. That code is the best answer.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Sean Davis25k
0
9 months ago by
chen1.7k
OpenGene
chen1.7k wrote:

This is per-cycle base content. R is not good at, and is not designed for such task.

Why complicate life? Just use fastp to do the easiest and fastest way for such tasks, including QC and filtering. It will output the figures like what you want.