{"id":1242,"date":"2014-01-20T10:38:52","date_gmt":"2014-01-20T10:38:52","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=1242"},"modified":"2016-02-23T11:50:28","modified_gmt":"2016-02-23T11:50:28","slug":"hicup","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/hicup\/","title":{"rendered":"HiCUP"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>HiCUP is a tool for mapping and performing quality control on Hi-C data.<\/p>\n<p>Version 0.5.8 and 0.4.2 are installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>HiCUP is open-source. All CSF users may access it.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>\r\nmodule load apps\/binapps\/hicup\/0.5.8\r\n\r\nOR\r\n\r\nmodule load apps\/binapps\/hicup\/0.4.2\r\n<\/pre>\n<p>You may also require <a href=\"\/csf-apps\/software\/applications\/bowtie\">bowtie<\/a> to be loaded when using this software.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run HiCUP on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Coming soon.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Coming soon.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/hicup\/\">HiCUP website<\/a>.<\/li>\n<li><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/hicup\/README.txt\">HiCUP README<\/a>.<\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview HiCUP is a tool for mapping and performing quality control on Hi-C data. Version 0.5.8 and 0.4.2 are installed on the CSF. Restrictions on use HiCUP is open-source. All CSF users may access it. Set up procedure To access the software you must first load the modulefile: module load apps\/binapps\/hicup\/0.5.8 OR module load apps\/binapps\/hicup\/0.4.2 You may also require bowtie to be loaded when using this software. Running the application Please do not run HiCUP.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/hicup\/\">Read more &raquo;<\/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-1242","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1242","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=1242"}],"version-history":[{"count":8,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1242\/revisions"}],"predecessor-version":[{"id":2895,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1242\/revisions\/2895"}],"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=1242"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}