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