FastQC for paired end data

Question

[Dk]

Hi, I have 36 fastq files of paired end RNA-seq so I was wondering if anyone knows how to do fastqc on paired-end data? and what is the difference between fastqc of single end data? I have done with single end data before but never with paired end so please help me. Thank you!

[cpad0112]

fastqc works with single files only. Do fastqc on all files and summarise multiple fastqc outputs with multiqc. Fastqc provides QC data as tsvs and you can parse them as per your requirements.

Answer 1

[MarkiMark]

you can do:

fastqc dir/of/files/sampleX_1.fastq.gz --outdir=/data/resfolder
fastqc dir/of/files/sampleX_2.fastq.gz --outdir=/data/resfolder

and put it in a loop if you don't want to do it manually for all files..

@liorglic mentioned MultiQC which is simpler to run

Answer 2

[liorglic]

Please search google and this forum before asking. See this post.
You may also want to take a look at MultiQC since you have a lot of reports to go through.