Hi ! This is my first time analysing ddRAD data, and I'd like to produce a multiQC report for all my 288 ddRAD samples. After demultiplexing reads from a ddRAD using stacks radtags you obtain 4 files per sample: 1) Sample_X.1.fq.gz 2) Sample_X.2.fq.gz 3) Sample_X.rem.1.fq.gz 4) Sample_X.rem.2.fq.gz They are, respectively, Sequences of the reads 1, Sequences of the reads 2, remaining sequences for read 1, remaining sequences for read 2.
My issue is, should I : 1) Run fastQC on all these files and obtain four fastQC reports per samples ? (This would give me a very messy multiQC report, not taking the paired end reads into account). 2) Concatenate the four files per samples in one file per samples, run fastQC on all of those and then multiQC on the corresponding reports? (I did that but obtained almost only 'duplicated reads' in the multiQC report so I suspect something went wrong in my procedure) 3) Something smarter ?!
Many thanks for your help! :) Noé