{"id":4470,"date":"2020-02-03T14:37:50","date_gmt":"2020-02-03T14:37:50","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4470"},"modified":"2025-09-10T10:45:34","modified_gmt":"2025-09-10T09:45:34","slug":"apt","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/apt\/","title":{"rendered":"Affymetrix Power Tools (APT)"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/www.thermofisher.com\/uk\/en\/home\/life-science\/microarray-analysis\/microarray-analysis-partners-programs\/affymetrix-developers-network\/affymetrix-power-tools.html\">Affymetrix Power Tools<\/a> (APT) is a set of cross-platform command line programs that implement algorithms for analyzing and working with GeneChip\u2122 arrays. APT programs are intended for &#8220;power users&#8221; who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>All users may access and use APT.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run APT commands on the login node. qrsh is recommended for some commands. Computationally intense work should be done via the batch system.<\/p>\n<h3>Examples<\/h3>\n<p>The following example first runs <code>apt<\/code> as a serial job.<\/p>\n<pre>#!\/bin\/bash --login\r\n#SBATCH -p serial    # (or --partition=) Use the nodes dedicated to 1-core jobs\r\n#SBATCH -t 4-0       # Wallclock limit of 4 days. Max permitted is 7-0.\r\n\r\nmodule purge\r\nmodule load apps\/binapps\/apt\/2.11.0\r\n\r\napt-probeset-summarize -a rma-sketch -a plier-mm-sketch  -p chip.pgf -c chip.clf -o output-dir *.cel\r\n<\/pre>\n<p>and submit the job using <code>qsub <em>jobscript<\/em><\/code> where jobscript is the name of your job script file.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/tools.thermofisher.com\/content\/sfs\/manuals\/axiom_genotyping_solution_analysis_guide.pdf\">APT Manual<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview Affymetrix Power Tools (APT) is a set of cross-platform command line programs that implement algorithms for analyzing and working with GeneChip\u2122 arrays. APT programs are intended for &#8220;power users&#8221; who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality. Restrictions on use All users may access and use APT. Running the application Please do not run APT commands on the login.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/apt\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":7,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4470","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4470","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=4470"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4470\/revisions"}],"predecessor-version":[{"id":10929,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4470\/revisions\/10929"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=4470"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}