I have 24 untrimmed fastq files for RNA-seq. They are paired files. I have them in a data collection and run fastQC on them with no problem, but when I try to aggregate fastQC results with multiQC it only reports two files; forward and reverse, instead of each of the 24 individual files. What I’m I doing wrong? I’ve followed the tutorials and have set all parameters per those tutorials but keep getting the same result.
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