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.
...
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 available on lonestar as a module.
...
| Expand | |||||
|---|---|---|---|---|---|
| |||||
|
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:
...
Let's look at tools to do such manipulations to fastqc files, if we have to.