Adapter content increases after trimming by Cutadapt
Hi, I have utilized Cutadapt to remove adapters from my ChIP-seq data. However, when I attempted to trim one of my datasets, the adapter content actually increased from 1% to 15% after trimming. This is quite unusual as I have never encountered this issue before. I typically use the default settings in usegalaxy, including a minimum length of 20 and a quality cutoff of 20. Could someone please provide insight into what might have gone wrong with my analysis? Thank you.
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Where? FastQC plot?