FastQC is a quality control tool for checking the quality of raw reads obtained from Next Generation sequencing platforms. It provides a modular set of analysis which gives a quick hint of quality of your data. It generates QC report in the form of graphs showing quality, N content, Adapter content, GC content present in your high throughput sequencing data. It can be downloaded from (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
FastQC can be run in different modes which are
FastQC can be run in different modes which are
- Standalone interactive application
- Non interactive mode
- By using galaxy which contains integrated FastQC tool
Working
1) Install the FastQC from above mentioned link. It can be installed on both LINUX as well as windows operating system. on linux it can be installed by using command
sudo apt-get [link of fastQC from where you are downloading]
sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc
fastqc somefile.txt
2) After installing FastQC now simply run the program and select File > Open. You can then select the files you want to analyse by using windows. But in LINUX use following command
fastqc somefile.txt
FastQC supports files in the following formats
- FastQ (all quality encoding variants)
- Casava FastQ files*
- Colorspace FastQ
- GZip compressed FastQ
- SAM
- BAM
- SAM/BAM
Shown below are some results obtained from FastQC
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