{"id":285,"date":"2022-08-04T15:23:55","date_gmt":"2022-08-04T15:23:55","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r-handbook-2022\/programme\/day-2\/raw-reads-to-expression-matrix\/"},"modified":"2025-03-18T11:52:06","modified_gmt":"2025-03-18T11:52:06","slug":"raw-reads-to-expression-matrix","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/processing-data\/raw-reads-to-expression-matrix\/","title":{"rendered":"Raw reads to expression matrix"},"content":{"rendered":"\n<p><strong>Trainers:<\/strong>&nbsp;Jiawei Wang and Jinzheng Ren<\/p>\n\n\n\n<p><strong>Overview:<\/strong>&nbsp;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<h2 class=\"wp-block-heading\"><strong>Materials<\/strong><\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2024\/ScRNA-seq-analysis-using-Python-2024\/6-Sc-RNA-seq_analysis\/1-Raw_data-to_matrix\/03_CellRangerSlides.pdf\">Presentation slides<\/a> for cellranger<\/li>\n\n\n\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2025\/Single_cell_rna_seq_analysis_using_python_2025\/Presentations\/JiaweiWang_EMBL_Raw%20reads%20to%20expression%20matrix_2025_02_18.pdf\">Main presentation slides<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Practical<\/strong><\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/github.com\/Functional-Genomics\/scRNA-seq_python_course_2024\" data-type=\"link\" data-id=\"https:\/\/github.com\/Functional-Genomics\/scRNA-seq_python_course_2024\">GitHub repository<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Trainers:&nbsp;Jiawei Wang and Jinzheng Ren Overview:&nbsp;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 Practical<\/p>\n","protected":false},"author":6,"featured_media":0,"parent":1947,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-285","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/pages\/285","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/comments?post=285"}],"version-history":[{"count":21,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/pages\/285\/revisions"}],"predecessor-version":[{"id":2337,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/pages\/285\/revisions\/2337"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/pages\/1947"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-materials\/wp-json\/wp\/v2\/media?parent=285"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}