FastQC<\/a> is a quality control tool for high throughput sequence data. The application is written in Java and can be used in batch or interactively (via the qrsh command).<\/p>\n Version 0.11.3 is installed on the CSF.<\/p>\n There are no restrictions on using this software on the CSF. The application is released under the GPL v3<\/a> license.<\/p>\n To access the software you must first load the modulefile:<\/p>\n Please do not run FastQC on the login node. Jobs should be submitted to the compute nodes via batch or run interactively via the qrsh command.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n FastQC can be run interactively but this must not<\/strong> be run on the login node. Instead you must schedule an interactive session on a compute node. Use the following commands (after loading the modulefile):<\/p>\n This will only run when a free core is available on one of the interactive nodes. If no free resources are available you will be asked to try again later.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview FastQC is a quality control tool for high throughput sequence data. The application is written in Java and can be used in batch or interactively (via the qrsh command). Version 0.11.3 is installed on the CSF. Restrictions on use There are no restrictions on using this software on the CSF. The application is released under the GPL v3 license. Set up procedure To access the software you must first load the modulefile: module load.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2483","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2483","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=2483"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2483\/revisions"}],"predecessor-version":[{"id":2484,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2483\/revisions\/2484"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=2483"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/binapps\/fastqc\/0.11.3\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\n# Specify a list of files to process\r\nfastqc inputfile1.txt inputfile2.txt\r\n\r\n# Note: If wishing to process compressed .fastq.gz file, use the following:\r\nzcat *fastq.gz | fastqc stdin\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Interactive use of the GUI<\/h3>\n
\r\nqrsh -l inter -l short -V fastqc\r\n<\/pre>\n
Further info<\/h2>\n
\n
\nless $FASTQC_HOME\/Install.txt\n<\/pre<\/li>\n
Updates<\/h2>\n