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FastQC is a tool that produces a quality analysis report on FASTQ files.
Useful links:
- FastQC report for a good Illumina dataset
- FastQC report for a bad Illumina dataset
- Online documentation for each FastQC report
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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.
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.
Note: For many of its reports, FastQC analyzes only the first 200,000 sequences in order to keep processing and memory requirements down.
Running FastQC
FastQC iis is available on stampede lonestar5 as a module.
Here's how to run FastQC on our sample data:
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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.