{"id":4477,"date":"2018-03-06T15:33:20","date_gmt":"2018-03-06T15:33:20","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4477"},"modified":"2018-03-06T15:35:58","modified_gmt":"2018-03-06T15:35:58","slug":"htseq","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/htseq\/","title":{"rendered":"HTSeq"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/htseq.readthedocs.io\/en\/release_0.9.1\/overview.html\">HTSeq<\/a> provides infrastructure to process data from high-throughput sequencing assays.<\/p>\n<p>Version 0.9.1 is installed on the CSF. This uses Anaconda Python v4.2.0 which provides Python 3.5.2.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing HTSeq on the CSF. The source is released under the GNU GPL v3 license.<\/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\/gcc\/python-packages\/anaconda3-4.2.0\/htseq\/0.9.0\r\n<\/pre>\n<p>The modulefile will automatically load the required version of Anaconda modulefile for you.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run HTSeq on the login node. Jobs should be submitted to the compute nodes via batch. <\/p>\n<p>Provided also are the binaries <\/p>\n<pre>htseq-count<\/pre>\n<p> and <\/p>\n<pre>htseq-qa<\/pre>\n<p>. You can also use it within a python script with import HTSeq.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\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\npython myscript.py\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>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/pypi.python.org\/pypi\/HTSeq\">HTSeq python docs<\/a><\/li>\n<li><a href=\"http:\/\/htseq.readthedocs.io\/en\/release_0.9.1\/\">HTSeq website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview HTSeq provides infrastructure to process data from high-throughput sequencing assays. Version 0.9.1 is installed on the CSF. This uses Anaconda Python v4.2.0 which provides Python 3.5.2. Restrictions on use There are no restrictions on accessing HTSeq on the CSF. The source is released under the GNU GPL v3 license. Set up procedure To access the software you must first load the modulefile: module load apps\/gcc\/python-packages\/anaconda3-4.2.0\/htseq\/0.9.0 The modulefile will automatically load the required version of.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/htseq\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":24,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4477","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4477","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\/24"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=4477"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4477\/revisions"}],"predecessor-version":[{"id":4481,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4477\/revisions\/4481"}],"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=4477"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}