This information is over 2 years old. Information was current at time of publication.{"id":2990,"date":"2018-11-09T11:00:55","date_gmt":"2018-11-09T16:00:55","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=2990"},"modified":"2018-11-26T10:02:06","modified_gmt":"2018-11-26T15:02:06","slug":"1114-wksp-rna-seq-clc-genomics","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2018\/11\/09\/1114-wksp-rna-seq-clc-genomics\/","title":{"rendered":"11\/14 wksp: RNA-Seq &amp; CLC Genomics"},"content":{"rendered":"<ul>\n<li><strong><span style=\"color: firebrick\">WHAT:<\/span> <\/strong>RNA-Seq &amp; CLC Genomics<\/li>\n<li><strong><span style=\"color: firebrick\">WHEN:<\/span> <\/strong>November 14th, 1-4 pm<\/li>\n<li><strong><span style=\"color: firebrick\">WHERE:<\/span> <\/strong>Scaife Hall, Falk Library, Classroom 2<\/li>\n<li><strong><span style=\"color: firebrick\">WHO:<\/span> <\/strong>Ansuman Chattopadhyay, PhD<\/li>\n<li><strong><span style=\"color: firebrick\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/molbio\/rna-seq-clc-genomics\/354\">here<\/a><\/li>\n<\/ul>\n<p><!--more-->Workshop Guide: <a href=\"http:\/\/hsls.libguides.com\/rnaseq\">http:\/\/hsls.libguides.com\/rnaseq<\/a><\/p>\n<p>Please register for <a href=\"http:\/\/hsls.libguides.com\/molbio\/clcgenomics\">CLC Genomics Workbench<\/a>.<\/p>\n<p>You must also sign up for a Center for Research Computing <a href=\"http:\/\/core.sam.pitt.edu\/apply\">HPC allocation<\/a>. Under &#8220;description&#8221; write <strong>CLC Genomics<\/strong>.<\/p>\n<p>This hands-on workshop is an introduction to RNA-Seq analysis using the library-licensed CLC Genomics Workbench. Participants will learn how to:<\/p>\n<ul>\n<li>import NGS reads from a published NCBI GEO dataset (GSE52778)<\/li>\n<li>perform quality control check on imported reads<\/li>\n<li>trim sequence reads based on quality score, adapter contamination, etc<\/li>\n<li>align RNA-Seq data to a reference genome<\/li>\n<li>calculate known genes and transcript expressions from mapped reads<\/li>\n<li>perform QC on mapping results<\/li>\n<li>perform differential expression analysis<\/li>\n<li>create visualization plots &#8211; Heatmap, Volcano Plot, Venn Diagram, etc<\/li>\n<li>display mapped reads alignment data in the context of the reference genome<\/li>\n<\/ul>\n<p><a href=\"http:\/\/files.hsls.pitt.edu\/files\/molbio\/MolbioWorkshops.pdf\">HSLS Fall 2018 MolBio Info Service Training Workshops schedule<\/a><\/p>\n<p>Please <a href=\"https:\/\/www.hsls.pitt.edu\/ask-a-molbio-specialist\">contact<\/a> the <a href=\"http:\/\/www.hsls.pitt.edu\/molbio\">HSLS Molecular Biology Information Service<\/a> with any questions.<\/p>\n","protected":false},"excerpt":{"rendered":"<ul>\n<li><strong><span style=\"color: firebrick\">WHAT:<\/span> <\/strong>RNA-Seq &amp; CLC Genomics<\/li>\n<li><strong><span style=\"color: firebrick\">WHEN:<\/span> <\/strong>November 14th, 1-4 pm<\/li>\n<li><strong><span style=\"color: firebrick\">WHERE:<\/span> <\/strong>Scaife Hall, Falk Library, Classroom 2<\/li>\n<li><strong><span style=\"color: firebrick\">WHO:<\/span> <\/strong>Ansuman Chattopadhyay, PhD<\/li>\n<li><strong><span style=\"color: firebrick\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/molbio\/rna-seq-clc-genomics\/354\">here<\/a><\/li>\n<\/ul>\n<p><a class=\"read-more\" alt= \"11\/14 wksp: RNA-Seq &amp; CLC Genomics\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2018\/11\/09\/1114-wksp-rna-seq-clc-genomics\/\">Read more&hellip;<\/a><\/p>\n","protected":false},"author":31,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[],"class_list":["post-2990","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/2990","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/users\/31"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/comments?post=2990"}],"version-history":[{"count":2,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/2990\/revisions"}],"predecessor-version":[{"id":2992,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/2990\/revisions\/2992"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=2990"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=2990"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=2990"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}