Sequence Duplication Levels Failed FastQC
I need help interpreting and fixing the Sequence Duplication Levels in my genomic data. We performed Illumina short read sequence for our whole genome. I ran FastQC on the data and it failed on two categories: GC content and Sequence Duplication. How can I adjust and fix the Sequence Duplication Levels as it is causing weird distributions in GenomeScope and KmerGenie. Attached is the Sequence Duplication Level distribution and GC Content distribution:
1 answer
Please see: https://sequencing.qcfail.com/articles/libraries-can-contain-technical-duplication/
Always keep the context of experiment in mind rather than going on "fails" in FastQC.
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