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  1. The Per base sequence quality report, which can help you decide if sequence trimming is needed before alignment.

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  1. The Sequence Duplication Levels report, which helps you evaluate library enrichment / complexity. But note that different experiment types are expected to have vastly different duplication profiles.
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  2. The Overrepresented Sequences report, which helps evaluate adapter contamination.
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titleA couple of other things to note about FastQC
  • For many of its reports, FastQC analyzes only the first 200,000 sequences in order to keep processing and memory requirements down.
  • Some of FastQC's graphs have a 1-100 vertical scale that is tricky to interpret. The 100 is a relative marker for the rest of the graph. For example, sequence duplication levels are relative to the number of unique sequences,

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