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DTSTAMP:20260617T195543Z
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DTSTART:20220927T040000Z
DTEND:20220927T070000Z
DESCRIPTION:RNA sequencing (RNA-seq) is a common method used to understand 
 the differences in gene expression and molecular pathways between two or m
 ore groups. This workshop introduces the fundamental concepts of RNA seque
 ncing experiments and will allow you to try out the analysis using data fr
 om a study of Williams-Beuren Syndrome\, a rare disease. \n\nIn the first 
 part of the workshop you will learn how to convert sequence reads into ana
 lysis ready count data. To do this we will use[ nf-core/rnaseq](https://nf
 -co.re/rnaseq/usage) - a portable\, scalable\, reproducible and publicly a
 vailable workflow on[ Pawsey Nimbus Cloud](https://pawsey.org.au/systems/n
 imbus-cloud-service/). In the second part of the workshop you will use the
  count data you created to identify differential genes and pathways using 
 R/Rstudio. By the end of the workshop\, you should be able to perform your
  own RNA-seq analysis for differential gene expression and pathway analysi
 s!\n\n**Lead Trainers:** Dr Nandan Deshpande\, Senior Research Bioinformat
 ician\, Sydney Informatics Hub\n\n**Date/Time**: 27 &amp\; 28 September 20
 22\, 2-5pm AEST/1:30-4:30pm ACST/12-3pm AWST \n\n**Format:**\n\nThis onlin
 e workshop will take place over two three-hour sessions. You must attend b
 oth sessions in order to get the most out of the workshop. Expert trainers
  will introduce new topics and guide you through hands-on activities to he
 lp you put your new skills into action.\n\n**Learning outcomes:**\n\nBy th
 e end of the workshop you should be able to:\n\n\n\n1. List the steps invo
 lved in analysis of RNA-seq data\n2. Describe key concepts and considerati
 ons for RNA-seq experiments \n3. Describe the benefits of using nf-core wo
 rkflows\n4. Deploy an RNA-seq nf-core workflow on Pawsey’s Nimbus Cloud 
 to perform:\n    1. Quality control\n    2. Alignment\n    3. Quantificati
 on to generate raw counts\n5. Use R/RStudio on Pawsey’s Nimbus Cloud to 
 perform\n    4. Quality control\n    5. Identify differentially expressed 
 genes using DESeq2\n    6. Perform functional enrichment/pathway analysis\
 n\n**Who the workshop is for:**\n\nThis workshop is for Australian researc
 hers who have or will work on RNAseq data as part of their projects. You m
 ust be associated with an Australian organisation for your application to 
 be considered.\n\nThe workshop will be conducted in a Unix environment and
  will use R/RStudio. \n\nBasic command line knowledge is required. You mus
 t know how to navigate the directory structure and copy files between the 
 computers. If you need a refresher on Unix/Linux try[ this online tutorial
 ](https://linuxjourney.com/lesson/the-shell).\n\nBasic knowledge of R/RStu
 dio is required. You must know how to set up directories\, run commands\, 
 reading in and outputting files.  If you need a refresher on R/RStudio try
  the[ Introduction to R and RStudio section](https://swcarpentry.github.io
 /r-novice-gapminder/01-rstudio-intro/index.html) of this online tutorial.\
 n\nIt’s recommended that you watch the webinar[ Portable\, reproducible 
 and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Clo
 ud](http://biocommons.org.au/events/nextflow-nimbus) in advance. You may j
 oin this webinar live on 20 September 2022. A recording will be posted on 
 the[ Australian BioCommons YouTube Channel](https://www.youtube.com/c/Aust
 ralianBioCommonsChannel).\n\n**How to apply:**\n\nThis workshop is free bu
 t participation is subject to application with selection. \n\nApplications
  close at **11:59pm AEST\, Sunday 11 September 2022**.\n\nApplications wil
 l be reviewed by the organising committee and all applicants will be infor
 med of the status of their application (successful\, waiting list\, unsucc
 essful). Successful applicants will be provided with a Zoom meeting link c
 loser to the date.\n\n**[Apply here](https://biocommons-rnaseq-2022.eventb
 rite.com.au/)**\n\n_This workshop is presented by the[ Australian BioCommo
 ns](https://www.biocommons.org.au/)\, Sydney Informatics Hub and Pawsey Su
 percomputing Research Centre with the assistance of a network of facilitat
 ors from the national[ Bioinformatics Training Cooperative](https://www.bi
 ocommons.org.au/training-cooperative)._\n\n_This event is part of a series
  of[ bioinformatics training events](https://www.biocommons.org.au/events)
 . If you'd like to hear when registrations open for other events\, please[
  subscribe](https://www.biocommons.org.au/subscribe) to Australian BioComm
 ons_\n
SUMMARY:WORKSHOP: RNA-Seq: reads to differential genes and pathways
URL;VALUE=URI:https://www.biocommons.org.au/events/rnaseq-2022
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