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DTSTART:20210520T100000Z
DTEND:20210521T153000Z
DESCRIPTION:This online course introduces the participants to microbiome an
 alysis methods\, tools\, and file formats. It covers the whole workflow fr
 om quality control and filtering to quantification and statistical analysi
 s using Mothur and Phyloseq tools integrated in the user-friendly Chipste
 r platform. Please note that this course focuses on microbiome analysis of
  amplicon sequencing data (as opposed to metagenomics where all the genes 
 are sequenced).The course consists of lectures and practical exercises. Th
 e lectures will be available as short videos\, and the participants are re
 quested to view them prior to the course. This gives you more time to refl
 ect on the concepts so that you can use the course days more efficiently. 
 The lectures are summarized and questions answered during the course.Learn
 ing outcomeAfter this course\, you will be able topreprocess amplicon sequ
 encing data for microbial community analysiscompare the structure of micro
 bial communities using ordinations and multivariate statisticsPrerequisite
 s and content levelThe free and user-friendly Chipster software is used in
  the exercises\, so no previous knowledge of Unix or R is required.The con
 tent level of the course is intermediate and the course is intended for
  life scientists who are planning to use 16S or other amplicon sequencing 
 in their microbiome research. This course is suitable also for those resea
 rchers who do not plan to analyze data themselves\, but who need to unders
 tand the concepts in order to discuss with bioinformaticians.AgendaDay 1\,
  Thursday May 20 (10:00 - 15:30 EEST | UTC/GMT + 3 hours)Checking the qual
 ity of reads with MultiQCPreprocessing combining paired reads to contigss
 creening sequences for length and ambiguous basesremoving identical sequen
 cesAlignmentaligning sequences to the Silva reference alignmentscreening a
 ligned sequences for alignment position and homopolymersfiltering alignmen
 t for empty columns and overhangsremoving new identical sequencesPrecluste
 ring\, removing chimeric sequencesDay 2\, Friday May 21 (10:00 - 15:30 EES
 T | UTC/GMT + 3 hours)Data tidying and analysisCreating and importing phyl
 oseq input filesIncluding taxonomic assignments and OTU clusteringData ins
 pection and tidying using phyloseqRemoving unwanted taxaFiltering singleto
 ns and doubletonsPrevalence filteringData transformation\, ordination and 
 conversionCLR\, Hellinger and % relative abundancenMDS and db-RDADESeq2 fo
 rmat conversion and variance-stabilising transformationRelative abundance 
 plotsCommunity comparisons using PERMANOVA\, PERMDISP and DESeq2Lecturers:
   Dr. Jesse Harrison (CSC)\, Dr. Eija Korpelainen (CSC)Language:  Englis
 hPrice:           Free of charge (2 training days)For further de
 tailed information please visit:https://events.prace-ri.eu/e/MicrobialComm
 unityAnalysisChipster_2021 THE COURSE IS FULLY BOOKED and REGISTRATION IS 
 CLOSED!If you have registered to the course and you are not able to attend
 \, please CANCEL your registration in advanceby sending an email to patc@c
 sc.fi.We have processed a limited waiting list. Please contact patc@csc.fi
  on that matter.We will keep those on the waiting list informed of whether
  participation will be possible.
LOCATION:Online event
SUMMARY:Online: Microbial community analysis with Chipster
URL;VALUE=URI:https://ssl.eventilla.com/event/xaB07
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