BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260618T132321Z UID:e0b3a476-36bb-4bef-9314-6e099a0a4046 DTSTART:20230508T000000Z DTEND:20230510T000000Z DESCRIPTION:**This course is now full with a long waiting list. If you do n ot want to miss your chance to be part of the next session and remain info rmed about all training activities at SIB\, we highly recommend you to kee p an eye on our list of [upcoming events](https://www.sib.swiss/training/u pcoming-training-courses) and subscribe to our courses [mailing list](http s://lists.sib.swiss/mailman/listinfo/courses) here (if you haven't done so already)**. \n\n\n\n\n\n# Overview\nThis three-day course will provide a n overview of the RNA-seq analysis pipeline\, as well as the downstream an alysis of the resulting data using bioconductor packages in R. The course will cover the following topics:\n\nThe structure of an RNAseq analysis pi peline:\n\nRaw data quality check\;\nRNAseq reads alignment\;\nGene Expres sion level quantification and normalization by reads counting\;\nDe novo T ranscripts reconstruction and differential splicing.\n\n\nOverview of down stream analysis\n\nDifferential Expression analysis with R/Bioconductor pa ckages\;\nClass discovery: usage of Principal Component Analysis\, Cluster ing\, Heatmaps\, Gene Set Enrichment Analysis in RNA-seq analysis.\n\n\n\n Next Generation Sequencing (NGS) techniques will not be covered in this co urse\; experimental design as well as the statistical methods will not be detailed in this course. \n\n\n# Audience\nLife scientists who are new in the RNA-seq data field but have some R and statistical knowledge.\n\n# Pre requisites\n\n### ***Knowledge / competencies***\n\nParticipants should al ready have a basic knowledge of Next Generation Sequencing (NGS) technique s\; this course will discuss only the data analysis steps and not the data generation.\nA basic knowledge in statistics is required. Participants sh ould know about p-values\, student T-test\, multiple testing correction an d classification\, PCA.\nA basic knowledge of R is also required. Particip ants should know how to read files\, run PCA\, do classification\, visuali se heatmaps using R command lines.\n A basis knowledge of Unix is also req uired.\n\n\n### ***Technical***\n\nA Wi-Fi enabled laptop with the latest version of R and Bioconductor installed. Participants with windows machi nes should have enabled WLS2\, so they can run linux software\n\n\n# Learn ing objectives\nAt the end of the course\, participants will be able to:\n \n\nrun a RNA-seq pipeline on a small dataset composed of two groups\;\n\n \ndescribe an RNA-seq experimental design\;\n\n\ndescribe pseudo-alignment s and alignment software\;\n\n\nestimate data quality\;\n\n\nnormalise cou nts\;\n\n\nknow and understand the essential steps of a simple gene expres sion analysis issued from RNA sequencing\;\n\n\nmanipulate gene expression matrices and differential expression tables\;\n\n\nperform a differential expression analysis based on R/Bioconductor packages (DeSeq2\, ...).\n\n\ n\n# Schedule\n\nDAY1 \n 9:00 - 10:30 - Introduction to RNA sequencing 10: 30 - 10:45 - Coffee Break 10:45 - 12:30 - RNAseq analysis pipeline\, part I 12:30 - 13:30 - Lunch Break 13:30 - 15:00 - RNAseq analysis pipeline\, p art II 15:00 - 15:15 - Coffee break 15:15 - 17:00 - Practicals \n\nDAY2 9:00 - 10:30 - Differential Expression analysis 10:30 - 10:45 - Coffee Bre ak 10:45 - 12:30 - Differential splicing 12:30 - 13:30 - Lunch Break 13:30 - 15:00 - Practicals 15:00 - 15:15 - Coffee break 15:15 - 17:00 – Pract icals \n\nDAY3 9:00 - 10:30 - Differential Expression analysis with DESEQ 2 10:30 - 10:45 - Coffee Break 10:45 - 12:30 - Downstream analysis 12:30 - 13:30 - Lunch Break 13:30 - 15:00 - Practicals 15:00 - 15:15 - Coffee bre ak 15:15 - 17:00 - Practicals \n \n \n\n# Application \n\nThis course is now full. \n\n\n\n\n\nRegistration fees are 300 CHF for academics and 150 0 CHF for for-profit companies.\nYou will be informed by email of your reg istration confirmation\, and you will be asked to complete the payment of the registration fees within 5 days.\nDeadline for registration and free-o f-charge cancellation is set to 24/04/2023. Cancellation after this date w ill not be reimbursed. Please note that participation in SIB courses is su bject to this and other general conditions\, available here.\n\n# Venue an d Time\n\n \n\nThis course will only be streamed online.\n \nIt will start at 9:00 CET and end around 17:00 CET.\n\nPrecise information will be prov ided to the participants before the course.\n# Additional information\nCoo rdination: Valeria Di Cola\, SIB Training Group.\nWe will recommend 0.75 E CTS credits for this course (given a passed exam at the end of the course) .\nYou are welcome to register to the SIB courses mailing-list to be infor med of all future courses and workshops\, as well as all important deadlin es using the form here.\nPlease note that participation in SIB courses is subject to our general conditions.\nSIB abides by the ELIXIR Code of Cond uct. Participants of SIB courses are also required to abide by the same co de.\nFor more information\, please contact training@sib.swiss. SUMMARY:Transcriptomics Analysis: RNA-seq URL;VALUE=URI:https://www.sib.swiss/training/course/20230508_RNASQ END:VEVENT END:VCALENDAR