Installing FastQC ------------------- OSX --- FastQC is distributed as a DMG image file. Download the image from the project page and double click it to open it. You should see the FastQC application appear in a Finder window. Drag the application from there to wherever you want to install it on your machine. Once you've copied the application double click it to open it. FastQC is not a signed application therefore it may initially be blocked by the Gatekeeper application. To avoid this open FastQC by right clicking on the app and selecting open. This may prompt you to allow it to open. If it is still blocked go to System Preferences > Security and Privacy and you should see an option to allow the application to open. You only need to do this once and the preference should be remembered by OSX. Windows and Linux ----------------- FastQC is a java application. In order to run it needs your system to have a suitable Java Runtime Environment (JRE) installed. Before you try to run FastQC you should therefore ensure that you have a suitable JRE. There are a number of different JREs available however the ones we have tested are the latest Oracle runtime environments and those from the adoptOpenJDK project (https://adoptopenjdk.net/). You need to download and install a suitable 64-bit JRE and make sure that the java application is in your path (most installers will take care of this for you). On linux most distributions will have java installed already so you might not need to do anything. If java isn't installed then you can add it by doing: Ubuntu / Mint: sudo apt install default-jre CentOS / Redhat: sudo yum install java-1.8.0-openjdk You can check whether java is installed by opening the 'cmd' program on windows, or any shell on linux and typing: java -version You should see something like: >java -version openjdk version "11.0.2" 2019-01-15 OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.2+9) OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.2+9, mixed mode) Actually installing FastQC is as simple as unzipping the zip file it comes in into a suitable location. That's it. Once unzipped it's ready to go. Running FastQC -------------- You can run FastQC in one of two modes, either as an interactive graphical application in which you can dynamically load FastQ files and view their results. Alternatively you can run FastQC in a non-interactive mode where you specify the files you want to process on the command line and FastQC will generate an HTML report for each file without launching a user interface. This would allow FastQC to be run as part of an analysis pipeline. Running FastQC Interactively ---------------------------- Windows: Simply double click on the run_fastqc bat file. If you want to make a pretty shortcut then we've included an icon file in the top level directory so you don't have to use the generic bat file icon. MacOSX: Double click on the FastQC application icon. Linux: We have included a wrapper script, called 'fastqc' which is the easiest way to start the program. The wrapper is in the top level of the FastQC installation. You may need to make this file executable: chmod 755 fastqc ..but once you have done that you can run it directly ./fastqc ..or place a link in /usr/local/bin to be able to run the program from any location: sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc Running FastQC as part of a pipeline ------------------------------------ To run FastQC non-interactively you should use the fastqc wrapper script to launch the program. You will probably want to use the zipped install file on every platform (even OSX). To run non-interactively you simply have to specify a list of files to process on the commandline fastqc somefile.txt someotherfile.txt You can specify as many files to process in a single run as you like. If you don't specify any files to process the program will try to open the interactive application which may result in an error if you're running in a non-graphical environment. There are a few extra options you can specify when running non-interactively. Full details of these can be found by running fastqc --help By default, in non-interactive mode FastQC will create an HTML report with embedded graphs, but also a zip file containing individual graph files and additional data files containing the raw data from which plots were drawn. The zip file will not be extracted by default but you can enable this by adding: --extract To the launch command. If you want to save your reports in a folder other than the folder which contained your original FastQ files then you can specify an alternative location by setting a --outdir value: --outdir=/some/other/dir/ If you want to run fastqc on a stream of data to be read from standard input then you can do this by specifing 'stdin' as the name of the file to be processed and then streaming uncompressed fastq format data to the program. For example: zcat *fastq.gz | fastqc stdin If you want the results from a streamed analysis sent to a file with a name other than stdin then you can add a colon and put the file name you want, for example: zcat *fastq.gz | fastqc stdin:my_results ..would write results to my_result.html and my_results.zip. Customising the report output ----------------------------- If you want to run FastQC as part of a sequencing pipeline you may wish to change the formatting of the report to add in your own branding or to include extra information. In the Templates directory you will find a file called 'header_template.html' which you can edit to change the look of the report. This file contains all of the header for the report file, including the CSS section and you can alter this however you see fit. Whilst you can make whatever changes you like you should probably leave in place the
structure of the html template since later code will expect to close the main div which is left open at the end of the header. There is no facility to change the code in the main body of the report or the footer (although you can of course change the styling). The text tags @@FILENAME@@ and @@DATE@@ are placeholders which are filled in when the report it created. You can use these placeholders in other parts of the header if you wish.