FastQC Quality ControlΒΆ
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
The main functions of FastQC are
- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application
See the FastQC home page for more info.
To run FastQC
on our data, simply type:
cd /vol/spool/tutorial-data
fastqc read1.fq read2.fq
After FastQC
finished running, copy the results to your public_html
directory:
cp -r read?.fq_fastqc ~/public_html/
Now you can access the report at:
http://<YOUR_AWS_IP_ADDRESS>/~ubuntu/read1.fq_fastqc/fastqc_report.html
http://<YOUR_AWS_IP_ADDRESS>/~ubuntu/read2.fq_fastqc/fastqc_report.html
Check out the FastQC home page for examples of reports including bad data.