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DTSTART:20251015T090000Z
DTEND:20251016T170000Z
DESCRIPTION:# Overview \nATAC-seq (Assay for Transposase-Accessible Chromat
 in using sequencing) is a powerful and widely used technique for profiling
  genome-wide chromatin accessibility. Highly accessible regions are typica
 lly enriched for active cis-regulatory elements\, including promoters\, en
 hancers\, and insulators. By quantifying transposase integration sites\, A
 TAC-seq enables the identification of these elements and the analysis of h
 ow accessibility patterns change across different biological conditions or
  perturbations\, helping to uncover mechanisms of gene regulation. \n\nThi
 s course will provide an introduction into ATAC-seq technology and its mai
 n applications to answer epigenetics related questions.  \n\nIt will also 
 cover main steps and available tools for the bioinformatics analysis of bu
 lk ATAC-seq data\, including: \n\n* Recap of the steps involved in process
 ing and aligning the raw reads\n* Quality control assessment specific to A
 TAC-seq \n* Peak calling\, annotation and visualisation \n* Differential a
 ccessibility (DA) analysis \n* Functional enrichment analysis of DA peaks 
 \n \n\nTheoretical and practical sessions will be combined to provide broa
 d context on ATAC-seq analysis methods as well as hands on experience usin
 g specific tools. \n\n \n \n\n# Audience \nThis course is addressed to lif
 e scientists and bioinformaticians familiar with “Next Generation Sequen
 cing” who want to acquire the necessary skills to process and analyse AT
 AC-seq data. \n \n \n# Learning outcomes \nAt the end of the course\, the 
 participants are expected to: \n* Explain the ATAC-seq technology\, its re
 ad-out and applications \n* Run and evaluate quality control measures spec
 ific to ATAC-seq technology \n* Perform the main steps to process an ATAC-
 seq dataset (from raw data to differential accessibility analysis) \n* Lis
 t other possible downstream analysis for ATAC-seq  \n \n \n# Prerequisites
  \n#### Knowledge / competencies \nThis course is designed for beginners a
 nd there is no requirement in previous knowledge analysing ATAC-seq or oth
 er epigenetics-related sequencing technologies.  \n \n\nParticipants must 
 already have a basic knowledge in **Next Generation Sequencing (NGS) techn
 iques**\, **R** (evaluate your R skills [here](https://docs.google.com/for
 ms/d/e/1FAIpQLSdIyeuabd_ZOWXgI1MWHapmaOMu20L9ESkLDZiWnpmkpujyOg/viewform?u
 sp=sf_link)) and **UNIX** (self-assess your skills with the e-learning cou
 rse [UNIX Fundamentals](https://www.sib.swiss/training/course/2012_UNIXF)\
 , and this [quiz](https://docs.google.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGB
 T_aDEGPce1FOaVYBbhBiaqcaHoBKNB27MQ/viewform?usp=sf_link)).\n\n \n\n#### Te
 chnical \nAttendees should have a Wi-Fi enabled computer and the [Integrat
 ive Genomics Viewer (IGV)](https://igv.org/doc/desktop/#DownloadPage/) ins
 talled.  \n\nAn online R and RStudio environment will be provided. In orde
 r to access that environment your computer needs to be able to access http
  websites (not https). You can check this by browsing this [website](http:
 //www.httpforever.com).\n\nHowever\, in case you wish to perform the pract
 ical exercises on your own computer\, please take a moment to install the 
 following before the course: \n\n* [R](https://cran.r-project.org) version
  &gt\; 4.2. \n* Latest RStudio version\, the [free version](https://rstudi
 o.com/products/rstudio/download/) is perfectly fine. \n \n \n \n\n\n \n \n
 \n# Application \n \nThe registration fees for academics are **200 CHF** a
 nd **1000 CHF** for for-profit companies. \n \nWhile participants are regi
 stered on a first come\, first served basis\, exceptions may be made to en
 sure diversity and equity\, which may increase the time before your regist
 ration is confirmed. \n \nApplications will close on *01/10/2025* or as so
 on as the places will be filled up. Deadline for free-of-charge cancellati
 on is set to *1/10/2025*. Cancellation after this date will not be reimbur
 sed.  \n \n\nYou will be informed by email of your registration confirmati
 on. Upon reception of the confirmation email\, participants will be asked 
 to confirm attendance by paying the fees within 5 days. \n \n \n\n# Venue 
 and Time \n \nThis course will take place in person only at the University
  of Bern. \n\nThe course will start at 9:00 CET and end around 17:00 CET. 
  \n \nPrecise information will be provided to the registered participants 
 in due time.  \n \n \n\n#  Additional information \nCoordination: Patricia
  Palagi \n \n \n\nWe will recommend 0.5 ECTS credits for this course (give
 n a passed exam at the end of the course). \n \n \n\nYou are welcome to re
 gister to the SIB courses mailing list to be informed of all future course
 s and workshops\, as well as all important deadlines using the form [here]
 (https://lists.sib.swiss/mailman/listinfo/courses). \n \n \n\nPlease note 
 that participation in SIB courses is subject to our [general conditions](h
 ttp://www.sib.swiss/training/terms-and-conditions). \n \n \n\nSIB abides b
 y the [ELIXIR Code of Conduct](https://elixir-europe.org/events/code-of-co
 nduct). Participants of SIB courses are also required to abide by the same
  code. \n \n \n\nFor more information\, please contact [training@sib.swiss
 ](mailto://training@sib.swiss).
SUMMARY:Introduction to NGS ATAC-seq data analysis
URL;VALUE=URI:https://www.sib.swiss/training/course/20251015_ATACS
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