How do I process a FASTQ file in RStudio?

Question

[bousbiat.ilhem]

I m a beginner in programming, and I was asked to process some fastq files downloaded from casement et al 2018. I found that I need to trim the reads as a start and continue processing the files afterwards. I am not sure how to do that, would you be able to assist me in that ?

[karl.stamm]

protip: if you don't know how to do something, search the task or goal, not the tool. You won't know which tools are appropriate, and asking how to do X using RStudio is foolish when the real question is 'how to do X'. There's probably a dozen other threads on this website and of course Google for how to trim the reads. Then we can talk about what do you mean by 'continue processing' because there's about infinite different tasks you may be getting into, hence bioinformatics is a field of study.

[swbarnes2]

Yup. First thing, saying you want to "process" something is meaningless. You need to learn what you actually need to do. .

Answer 1

[JC]

you don't use R for this, there are many tools for trimming:

• First check if you need to trim with a report with FastQC
• Options for trimming: CutAdapt, Trimmomatic