How to do Fastq quality control on paired-end samples?

Question

[gbmygbm]

Dear community:

I have a set of paired-end data (like X_1.fq and X_2.fq) and I want to know the quality of their sequencing. I searched on the Internet and the community and find that fastQC is not proper for PE analyze. So what is the next step for doing QC on PE? Maybe I could merge the two files by samtools or other tools then use fastQC? Or if there are any other software for this situation? I'm looking for your advice and thanks in advance!

Answer 1

[ATpoint]

Just run fastqc X_1.fq and fastqc X_2.fq and be done with it. The entire world uses that tools for PE data. Whatever you read there is either wrong or not fully in context.