fastqc for Debian ----------------- 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. Configuration ------------- Configuration files have been placed in /etc/fastqc/Configuration Running FastQC Interactively ---------------------------- A wrapper is installed into /usr/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. 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 both a zipped copy of the QC report, and also extract this to create a folder which contains the report files ready to be viewed. If you only want to create the zipped file then you can add --noextract To the launch command to suppress the unzipping. 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/ 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. If you want to add in your own logo or other image files to the reports then you can drop a png or jpg file into the Icons folder in the templates directory and this will be copied into the report folder for all reports generated by the program. You can refer to these icons using a relative URL (eg Icons/image.png) in the HTML template. Images placed outside the icons directory will not be copied. 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. -- Andreas Tille Wed, 07 Nov 2012 14:24:25 +0100