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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.
DETOUR: What are PCR duplicates?
- The Overrepresented Sequences report, which helps look for dominant sequences.
5. Adapter content report, which tells you about adapter contamination.
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module load biocontainers
module load fastqc
fastqc data/Sample1_R1.fastq |
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You can't run a web browser directly from your "dumb terminal" command line environment. The FastQC results have to be placed where a web browser can access them. We put a copy at this URL:
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| title | FastQC results URL |
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transferred to your computer to look at the html report.
Exercise: Should we trim this data?
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The Per base sequence quality report shows that trimming the last 10 bp or so would not bases may be a bad good idea. |
Let's look at tools to do such manipulations to fastqc files, if we have to.