Saving a Report

In addition to providing an interactive report FastQC also has the option to create an HTML version of this report for a more permanent record. This HTML report can also be generated directly by running FastQC in non-interactive mode.

To create a report simply select File > Save Report from the main menu. By default a report will be created using the name of the fastq file with _fastqc.html appended to the end. The report will be created for whichever file tab was active when the menu option was selected.

The HTML file which is saved is a self-contained document with all of the graphs embedded into it, so you can distribute this single file. Alongside the HTML file is a zip file (with the same name as the HTML file, but with .zip added to the end). This file contains the graphs from the report as separate files but also contains data files which are designed to be easily parsed to allow for a more detailed and automated evauation of the raw data on which the QC report is built.