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DTSTAMP:20260711T100332Z
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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. These accessible regions are typical
 ly enriched for active cis-regulatory elements\, including promoters\, enh
 ancers\, and insulators. By quantifying transposase integration sites\, AT
 AC-seq enables the identification of these elements and the analysis of ho
 w accessibility patterns change across different biological conditions or 
 perturbations\, helping to uncover mechanisms of gene regulation \n\nThis 
 course will provide an introduction into ATAC-seq technology and its main 
 applications to answer epigenetics related questions.  \n\nIt will also co
 ver main steps and available tools for the bioinformatics analysis of bulk
  ATAC-seq data\, including: \n\n* Pre-processing of raw reads and quality 
 control assessment \n* Alignment of reads to reference genome \n* Peak cal
 ling\, annotation and visualisation \n* Differential accessibility (DA) an
 alysis \n* Functional enrichment analysis of DA peaks \n \n\nTheoretical a
 nd practical sessions will be combined to provide broad context on ATAC-se
 q analysis methods as well as hands on experience using specific tools. \n
 \n \n \n\n# Audience \nThis course is addressed to life scientists and bio
 informaticians familiar with “Next Generation Sequencing” who want to 
 acquire the necessary skills to process and analyse ATAC-seq data. \n \n \
 n# Learning outcomes \nAt the end of the course\, the participants are exp
 ected to: \n* Explain the ATAC-seq technology\, its read-out and applicati
 ons \n* Run and evaluate quality control measures specific to ATAC-seq tec
 hnology \n* Perform the main steps to process an ATAC-seq dataset (from ra
 w data to differential accessibility analysis) \n* List other possible dow
 nstream analysis for ATAC-seq  \n \n \n# Prerequisites \n#### Knowledge / 
 competencies \nThis course is designed for beginners and there is no requi
 rement in previous knowledge analysing ATAC-seq or other epigenetics-relat
 ed sequencing technologies.  \n \nParticipants must already have a basic k
 nowledge in Next Generation Sequencing (NGS) techniques\, R (evaluate your
  R skills here) and UNIX (self-assess your skills with the e-learning cour
 se UNIX Fundamentals\, and this quiz). \n \n \n \n\n#### Technical \nAtten
 dees should have a laptop with a command line terminal installed. An onlin
 e R and RStudio environment will be provided. However\, in case you wish t
 o perform the practical exercises on your own computer\, please take a mom
 ent to install the following before the course: \n\n* R version &gt\; 4.2.
  \n* Latest RStudio version\, the free version is perfectly fine. \n \n \n
  \n\n\n \n \n\n# Application \n \nThe registration fees for academics are 
 **200 CHF** and **1000 CHF** for for-profit companies. \n \nWhile particip
 ants are registered on a first come\, first served basis\, exceptions may 
 be made to ensure diversity and equity\, which may increase the time befor
 e your registration is confirmed. \n \nApplications will close on *24/09/2
 025* or as soon as the places will be filled up. Deadline for free-of-char
 ge cancellation is set to *1/10/2025*. Cancellation after this date will n
 ot be reimbursed.  \n \n\nYou will be informed by email of your registrati
 on confirmation. Upon reception of the confirmation email\, participants w
 ill 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 t
 he University of Bern. \n\nThe course will start at 9:00 CET and end aroun
 d 17:00 CET.  \n \nPrecise information will be provided to the registered 
 participants in due time.  \n \n \n\n#  Additional information \nCoordinat
 ion: Patricia Palagi \n \n \n\nWe will recommend 0.5 ECTS credits for this
  course (given a passed exam at the end of the course). \n \n \n\nYou are 
 welcome to register to the SIB courses mailing list to be informed of all 
 future courses and workshops\, as well as all important deadlines using th
 e 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](http://www.sib.swiss/training/terms-and-conditions). \n \n \n\
 nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europe.org/even
 ts/code-of-conduct). Participants of SIB courses are also required to abid
 e by the same code. \n \n \n\nFor more information\, please contact [train
 ing@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Introduction to NGS ATAC-seq data analysis
URL;VALUE=URI:https://www.sib.swiss/training/course/20251015_ATAQS
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