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DTSTAMP:20260711T095120Z
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DTSTART:20261014T090000Z
DTEND:20261015T170000Z
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 designed for PhD
  students\, postdoctoral and other researchers in the life sciences from b
 oth academia and industry familiar with “Next Generation Sequencing” w
 ho want to acquire the necessary skills to process and analyse ATAC-seq da
 ta. \n \n \n# Learning outcomes \nAt the end of the course\, the participa
 nts are expected to: \n* Explain the ATAC-seq technology\, its read-out an
 d applications \n* Run and evaluate quality control measures specific to A
 TAC-seq technology \n* Perform the main steps to process an ATAC-seq datas
 et (from raw data to differential accessibility analysis) \n* List other p
 ossible downstream analysis for ATAC-seq  \n \n \n# Prerequisites \n#### K
 nowledge / competencies \nThis course is designed for beginners and there 
 is no requirement in previous knowledge analysing ATAC-seq or other epigen
 etics-related sequencing technologies.  \n \n\nParticipants must already h
 ave a basic knowledge in **Next Generation Sequencing (NGS) techniques**\,
  **R** (evaluate your R skills [here](https://docs.google.com/forms/d/e/1F
 AIpQLSdIyeuabd_ZOWXgI1MWHapmaOMu20L9ESkLDZiWnpmkpujyOg/viewform?usp=sf_lin
 k)) and **UNIX** (self-assess your skills with the e-learning course [UNIX
  Fundamentals](https://www.sib.swiss/training/course/2012_UNIXF)\, and thi
 s [quiz](https://docs.google.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce
 1FOaVYBbhBiaqcaHoBKNB27MQ/viewform?usp=sf_link)).\n\n \n\n#### Technical \
 nAttendees should have a Wi-Fi enabled computer and the [Integrative Genom
 ics Viewer (IGV)](https://igv.org/doc/desktop/#DownloadPage/) installed.  
 \n\nAn online R and RStudio environment will be provided. In order to acce
 ss that environment your computer needs to be able to access http websites
  (not https). You can check this by browsing this [website](http://www.htt
 pforever.com).\n\nHowever\, in case you wish to perform the practical exer
 cises 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://rstudio.com/pro
 ducts/rstudio/download/) is perfectly fine. \n \n \n \n\n\n \n \n\n# Appli
 cation \n \nThe registration fees for academics are **200 CHF** and **1000
  CHF** for for-profit companies. \n \nWhile participants are registered on
  a first come\, first served basis\, exceptions may be made to ensure dive
 rsity and equity\, which may increase the time before your registration is
  confirmed. \n \nApplications will close on *01/10/2025* or as soon as the
  places will be filled up. Deadline for free-of-charge cancellation is set
  to *1/10/2025*. Cancellation after this date will not be reimbursed.  \n 
 \n\nYou will be informed by email of your registration confirmation. Upon 
 reception of the confirmation email\, participants will be asked to confir
 m 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 \nPre
 cise information will be provided to the registered participants in due ti
 me.  \n \n \n\n#  Additional information \nCoordination: Geert van Geest\,
  SIB Training Group\n \n \n\nWe will recommend 0.5 ECTS credits for this c
 ourse (given a passed exam at the end of the course). \n \n \n\nYou are we
 lcome to register to the SIB courses mailing list to be informed of all fu
 ture courses and workshops\, as well as all important deadlines using the 
 form [here](https://lists.sib.swiss/mailman/listinfo/courses). \n \n \n\nP
 lease note that participation in SIB courses is subject to our [general co
 nditions](http://www.sib.swiss/training/terms-and-conditions). \n \n \n\nS
 IB abides by the [ELIXIR Code of Conduct](https://elixir-europe.org/events
 /code-of-conduct). Participants of SIB courses are also required to abide 
 by the same code. \n \n \n\nFor more information\, please contact [trainin
 g@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Introduction to NGS ATAC-seq data analysis
URL;VALUE=URI:https://www.sib.swiss/training/course/20261014_ATACS
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