I am trying to compare the output files of Trimmomatic using FastQC and ultimately MultiQC. FastQC is able to assess the trimmed, paired reads, but not the trimmed unpaired reads; I have tried several times, and the runs fail every time. Is there a reason why this shouldn’t work? In the past, it has seemed that Trimmomatic works better with unpaired reads, but I would like to prove this by looking at the quality statistics.
Thank you for your help!