The Quality_Assessment handler runs FastQC on a list of FASTQ samples. FastQC can process any type of FASTQ encoding and can handle sample inputs that are gzipped or bzipped. Running Quality_Assessment will produce a HTML document for each sample and a summary file for all samples containing metrics on the sequence quality, sequence length distribution, sequence duplication levels, adapter content, and other quality statistics. For more information on these metrics, view the FastQC documentation.

To run Quality_Assessment, all common and handler-specific variables must be defined within the configuration file. Once the variables have been defined, Quality_Assessment can be submitted to a job scheduler with the following command (assuming that you are in the directory containing RNApipeline):

./main.sh Quality_Assessment proj.conf

The following are a list of variables that need to be defined within the configuration file. In addition to the handler-specific variables, all common variables must be defined.

Quality_Assessment will output a HTML and a zip file for each sample in your raw sample list using FastQC. To view the HTML files, open them using your favorite web browser.

The Quality_Assessment handler depends on:

• FastQC
• GNU Parallel
• The Grid Engine