{"id":4112,"date":"2019-10-07T11:51:06","date_gmt":"2019-10-07T10:51:06","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4112"},"modified":"2019-10-07T11:54:05","modified_gmt":"2019-10-07T10:54:05","slug":"subread","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/subread\/","title":{"rendered":"subread"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>Subread is a a tool kit for processing next-gen sequencing data.<\/p>\n<p>Version 2.0.0 is installed on the CSF3. It was compiled with Intel Compilers 18 (using <code>-msse2 -axSSE4.2,AVX,CORE-AVX2,CORE-AVX512)<\/code><\/p>\n<h2>Restrictions on use<\/h2>\n<p>This software is open-source so all CSF users may use it.<\/p>\n<p>If you use the Subread or Subjunc aligners, please cite:<br \/>\n<em>Liao Y, Smyth GK and Shi W (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108<\/em><\/p>\n<p>If you use the featureCounts program, please cite:<br \/>\n<em>Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30.<\/em><\/p>\n<h2>Set up procedure<\/h2>\n<p>For single (up to 32 core)\u00a0 jobs:<\/p>\n<pre>module load apps\/intel-18.0\/subread\/2.0.0\r\n<\/pre>\n<h2>Running the application<\/h2>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li>Please do not run subread on the login node.<\/li>\n<li>All Jobs should be submitted to the compute nodes via batch.<\/li>\n<li>The <code>$NSLOTS<\/code> in the examples is important as it ensures correct utilisation of resources.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><!--\n \t\n\n<li>This software will not run on the AMD nodes.<\/li>\n\n\n--><\/p>\n<h3>Parallel batch job submission &#8211; up to 32 cores on a (single compute node)<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -V\r\n#$ -pe smp.pe 5\r\n\r\nmodule load apps\/intel-18.0\/subread\/2.0.0\r\n\r\nsubread-align -T $NSLOTS -i my_index -r input.file -t 1 -o output.file\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. <!--Note: the <code>--bind-to none<\/code> is important for small mpi jobs on the CSF.--><\/p>\n<h2><\/h2>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/bioinf.wehi.edu.au\/subread\/\">Subread website<\/a><\/li>\n<li><a href=\"http:\/\/bioinf.wehi.edu.au\/subread-package\/SubreadUsersGuide.pdf\">Users guide (pdf)<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Subread is a a tool kit for processing next-gen sequencing data. Version 2.0.0 is installed on the CSF3. It was compiled with Intel Compilers 18 (using -msse2 -axSSE4.2,AVX,CORE-AVX2,CORE-AVX512) Restrictions on use This software is open-source so all CSF users may use it. If you use the Subread or Subjunc aligners, please cite: Liao Y, Smyth GK and Shi W (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research,.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/subread\/\">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-4112","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4112","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=4112"}],"version-history":[{"count":5,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4112\/revisions"}],"predecessor-version":[{"id":4118,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4112\/revisions\/4118"}],"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=4112"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}