{"id":192,"date":"2021-07-27T13:53:17","date_gmt":"2021-07-27T13:53:17","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-materials\/further-learning\/raw-reads-to-expression-matrix\/"},"modified":"2023-01-10T16:23:55","modified_gmt":"2023-01-10T16:23:55","slug":"raw-reads-to-expression-matrix","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/processing-data\/raw-reads-to-expression-matrix\/","title":{"rendered":"Raw reads to expression matrix"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><strong>Trainers:<\/strong> <a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/trainers-biographies\/\">Iguaracy Pinheiro de Sousa and\u00a0Daniel O\u2019Hanlon<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong> This session will focus on how to perform the initial alignment of the raw reads to the genome, to get an Expression Matrix (EM) in the end.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Materials:<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/docs.google.com\/presentation\/d\/1-F9g7t3cX3EWReC93oZ1FLjT3DTGdH7I\/edit?usp=sharing&amp;ouid=107001233493882804410&amp;rtpof=true&amp;sd=true\" target=\"_blank\" rel=\"noreferrer noopener\">Presentation slides<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Practical<\/strong>:<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/gist.github.com\/dpohanlon\/daf7676f19c2f25e02f79496531d3ed2\" target=\"_blank\" rel=\"noreferrer noopener\">Tutorial<\/a><br><br>Tutorial screencast:<\/p>\n\n\n\n<iframe loading=\"lazy\" src=\"https:\/\/embl-ebi.cloud.panopto.eu\/Panopto\/Pages\/Embed.aspx?id=6626b1f1-3f39-4180-8fb5-af2700f57560&amp;autoplay=false&amp;offerviewer=true&amp;showtitle=true&amp;showbrand=true&amp;captions=false&amp;interactivity=all\" height=\"405\" width=\"720\" style=\"border: 1px solid #464646;\" allowfullscreen=\"\" allow=\"autoplay\"><\/iframe>\n\n\n\n<p class=\"wp-block-paragraph\"><a rel=\"noreferrer noopener\" href=\"https:\/\/gist.github.com\/dpohanlon\/29af8b2cf0be2bd6d5b100e2e3bca402\" target=\"_blank\">Repository<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/drive.google.com\/drive\/folders\/1Tb1nBkIZEDyVnY8PPIJ7DwOtF0B5z-bC?usp=sharing\" target=\"_blank\" rel=\"noreferrer noopener\">Data<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Trainers: Iguaracy Pinheiro de Sousa and\u00a0Daniel O\u2019Hanlon Overview: This session will focus on how to perform the initial alignment of the raw reads to the genome, to get an Expression Matrix (EM) in the end. Materials: Presentation slides Practical: Tutorial Tutorial screencast: Repository Data<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":22,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-192","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/192","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/comments?post=192"}],"version-history":[{"count":12,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/192\/revisions"}],"predecessor-version":[{"id":815,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/192\/revisions\/815"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/22"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/media?parent=192"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}