Issues analysing splitted fastq files with fastqc

Question

[youssef.snoussi1994]

Hello, I've downloaded some fastq files using fastq-dump --splt-files which results in 2 fastq files; the problem i have is that i don't know what's the meaning of each file and how i can analyse them with fastqc. can anyone help

Answer 1

[benformatics]

FastQC only works on individual files and doesn't take into account paired end sequencing.

fastqc *fastq,gz

or

fastqc *fastq

Depending on the files you have, one of these should generate the standard quality control output for each of all the files you downloaded.

[youssef.snoussi1994]

So should I just download one file and work with it ?

[GenoMax]

You need to QC paired-end data files independently. So there will be two QC files to look through once you do what @benformatics said above.