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- The Per base sequence quality report, which can help you decide if sequence trimming is needed before alignment.
2. The Per Sequence Quality Score report, which can tell you if a subset of your reads just have poor quality scores. These reads can be completely filtered from analysis.
3. 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.
- The Overrepresented Sequences report, which helps evaluate look for dominant sequences.
5. Adapter content report, which tells you about adapter contamination.
Note: For many of its reports, FastQC analyzes only the first 200,000 sequences in order to keep processing and memory requirements down.
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