The first order of business after receiving sequencing data should be to check your data quality. This often-overlooked step helps guide the manner in which you process the data, and can prevent many headaches.
FastQC
FastQC is a tool that produces a quality analysis report on FASTQ files.
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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 adapter contamination.
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| title | A couple of other things to note about FastQC |
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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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Running FastQC
FastQC iis available on lonestar as a module.
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Looking at FastQC output
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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Let's look at tools to do such manipulations to fastqc files, if we have to.