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QC Reads with FastQC

Description:

We will do a quality check to verify the sequencing data is of suitable quality for downstream analysis.

Input Data:

Input Description Example
fastq_file_metadata.csv A CSV file containing metadata labels for the FastQ files FastQ metadata

Use FastQC App to Report on Sequence Quality

  1. In the Discovery Environment click on the Data icon and navigate to your rna-seq-tutorial tutorial folder and create a folder to store outputs, name the folder fastqc_analyses.
  2. In the Apps view, search for and launch the FastQC 0.11.5 (multi-file) app. You can use this direct link: FastQC app
  3. In Analysis Info you can name this analysis and provide any comments (optional). Under Output folder, navigate to the fastqc_analyses folder created earlier. Your outputs will automatically be placed in this folder; click Next.
  4. In Parameters for Input browse to the fastq_files folder previously created and add the 12 files (e.g., SRR9666131.sra.fastq, SRR9666132.sra.fastq); click Next.
  5. Click Next again to skip Advanced Settings (optional); under Review and Launch click Launch Analysis.
  6. Click on Analyses view to see the current status of the job; you can also click on the Analyses icon to navigate to this section. When the job is complete, you can click on the folder icon next to the analyses name to browse the results. You may need to Refresh to see the current job status. This job is expected to take 30-40 minutes.
  7. When the job has status Completed, navigate to the output. The expected output will be 12 HTML formatted reports, and 12 zip files containing additional files including text-based metrics. You can click on and examine all the HTML files; they will open as new tabs in your web browser. Review of the example dataset indicates the samples are all of high quality and additional filtering or trimming would not improve our quantification results.

Output/Results

Output Description Example
HTML and ZIP files of FastQC reports For each FastQ file an HTML file with an interactive report on sequence quality and a ZIP file with components of that report are created. FastQC Reports

Description of output and results

In the case of the tutorial data, the sequence quality is of very high quality. If necessary, other applications (e.g. Trimmomatic) could be used at this stage to do further filtering or trimming.

Last update: 2022-11-28