{"id":7975,"date":"2024-09-16T12:35:18","date_gmt":"2024-09-16T11:35:18","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=7975"},"modified":"2024-09-16T12:37:05","modified_gmt":"2024-09-16T11:37:05","slug":"kas-analyzer","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/kas-analyzer\/","title":{"rendered":"KAS-Analyzer"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>KAS-Analyzer is a comprehensive framework for exploring KAS-seq data<\/p>\n<p>KAS-Analyzer is a newly designed, comprehensive methodological framework aimed at simplifying the analysis and interpretation of KAS-seq data. In addition to standard analyses, KAS-Analyzer offers many novel features specifically tailored for KAS-seq data, including, but not limited to: calculation of termination length and index, identification of single-stranded transcribing (SST) enhancers, high-resolution mapping of R-loops, and time-course differential RNA polymerase activity analysis.<\/p>\n<p>KAS-Analyzer is still on active development and the source code is hosted on GitHub.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>KAS-Analyzer code is licensed under the <a href=\"https:\/\/github.com\/Ruitulyu\/KAS-Analyzer#MIT-1-ov-file\">MIT License<\/a> and is available on <a href=\"https:\/\/github.com\/Ruitulyu\/KAS-Analyzer\">Github<\/a>.<\/p>\n<h2>Set up procedure<\/h2>\n<p>We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.<\/p>\n<p>Load one the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/python\/kas-analyzer\/2.0\r\n<\/pre>\n<p>Then activate the environment:<\/p>\n<pre>\r\nsource activate \/opt\/apps\/apps\/python\/kas-analyzer\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run KAS-Analyzer on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n\r\n\r\n# Load the module and activate the environment\r\nmodule load apps\/python\/kas-analyzer\/2.0\r\nsource activate \/opt\/apps\/apps\/python\/kas-analyzer\r\n\r\nKAS-Analyzer download -a bowtie2 -g hg19 -d \/path\/to\/download\/directory\r\n\r\n<\/pre>\n<p>Submit the jobscript using:<\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Additional usage info<\/h2>\n<p>There is no need for using <strong><em>nohup<\/em><\/strong> at the begining and <strong><em>&#038;<\/em><\/strong> at the end<br \/>\nas shown in some of the examples in <a href=\"https:\/\/ruitulyu.github.io\/KAS-Analyzer\/\">KAS-Analyzer Documentation<\/a>.<\/p>\n<p>Please do not try to run <strong>install<\/strong> and <strong>uninstall<\/strong> commands as they will not work.<br \/>\nAll necessary tools are already installed and ready to use.<\/p>\n<p>Also, please do not use <strong>conda activate KAS-Analyzer<\/strong>,<br \/>\nwe use <strong>source activate \/opt\/apps\/apps\/python\/kas-analyzer<\/strong> here instead.<\/p>\n<h2>Further info<\/h2>\n<p><a href=\"https:\/\/ruitulyu.github.io\/KAS-Analyzer\/\">KAS-Analyzer Documentation<\/a><br \/>\n<a href=\"https:\/\/github.com\/Ruitulyu\/KAS-Analyzer\">KAS-Analyzer Github<\/a><\/p>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview KAS-Analyzer is a comprehensive framework for exploring KAS-seq data KAS-Analyzer is a newly designed, comprehensive methodological framework aimed at simplifying the analysis and interpretation of KAS-seq data. In addition to standard analyses, KAS-Analyzer offers many novel features specifically tailored for KAS-seq data, including, but not limited to: calculation of termination length and index, identification of single-stranded transcribing (SST) enhancers, high-resolution mapping of R-loops, and time-course differential RNA polymerase activity analysis. KAS-Analyzer is still on.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/kas-analyzer\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":21,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-7975","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/7975","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\/21"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=7975"}],"version-history":[{"count":9,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/7975\/revisions"}],"predecessor-version":[{"id":7984,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/7975\/revisions\/7984"}],"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=7975"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}