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DTSTART:20210520T070000Z
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DESCRIPTION:\nThis course was delivered as an ONLINE COURSE for remote part
 icipation \ndue to the COVID-19 measures enforced by most European govern
 ments.\n\n\nDescription\n\n\nThis online course introduces the participant
 s to microbiome analysis methods\, tools\, and file formats. It covers the
  whole workflow from quality control and filtering to quantification and s
 tatistical analysis using Mothur and Phyloseq tools integrated in the use
 r-friendly Chipster platform. Please note that this course focuses on micr
 obiome analysis of amplicon sequencing data (as opposed to metagenomics wh
 ere all the genes are sequenced).\n\nThe course consists of lectures and p
 ractical exercises. The lectures will be available as short videos\, and t
 he participants are requested to view them prior to the course. This gives
  you more time to reflect on the concepts so that you can use the course d
 ays more efficiently. The lectures are summarized and questions answered d
 uring the course.\n\n\nLearning outcome\n\nAfter this course\, you will be
  able to\n\n\n	\n	preprocess amplicon sequencing data for microbial commun
 ity analysis\n	\n	\n	compare the structure of microbial communities using 
 ordinations and multivariate statistics\n	\n\n\nPrerequisites and content 
 level\n\nThe free and user-friendly Chipster software is used in the exerc
 ises\, so no previous knowledge of Unix or R is required.\n\nThe content l
 evel of the course is intermediate and the course is intended for life 
 scientists who are planning to use 16S or other amplicon sequencing in the
 ir microbiome research. This course is suitable also for those researchers
  who do not plan to analyze data themselves\, but who need to understand t
 he concepts in order to discuss with bioinformaticians.\n\n\nAgenda\n\nDay
  1\, Thursday May 20 (10:00 - 15:30 EEST | UTC/GMT + 3 hours)\n\n\n	\n	Che
 cking the quality of reads with MultiQC\n	\n	\n	Preprocessing \n\n	\n		\n
 		combining paired reads to contigs\n		\n		\n		screening sequences for len
 gth and ambiguous bases\n		\n		\n		removing identical sequences\n		\n	\n	\
 n	\n	Alignment\n\n	\n		\n		aligning sequences to the Silva reference align
 ment\n		\n		\n		screening aligned sequences for alignment position and hom
 opolymers\n		\n		\n		filtering alignment for empty columns and overhangs\n
 		\n		\n		removing new identical sequences\n		\n	\n	\n	\n	Preclustering\, 
 removing chimeric sequences\n	\n\n\nDay 2\, Friday May 21 (10:00 - 15:30 E
 EST | UTC/GMT + 3 hours)\n\n\n	Data tidying and analysis\n	\n	Creating and
  importing phyloseq input files\n\n	\n		\n		Including taxonomic assignment
 s and OTU clustering\n		\n	\n	\n	\n	Data inspection and tidying using phyl
 oseq\n\n	\n		\n		Removing unwanted taxa\n		\n		\n		Filtering singletons an
 d doubletons\n		\n		\n		Prevalence filtering\n		\n	\n	\n	\n	Data transform
 ation\, ordination and conversion\n\n	\n		\n		CLR\, Hellinger and % relati
 ve abundance\n		\n		\n		nMDS and db-RDA\n		\n		\n		DESeq2 format conversio
 n and variance-stabilising transformation\n		\n	\n	\n	\n	Relative abundanc
 e plots\n	\n	\n	Community comparisons using PERMANOVA\, PERMDISP and DESeq
 2\n	\n\n\n\nLecturers:  \n\nDr. Jesse Harrison (CSC)\, Dr. Eija Korpelain
 en (CSC)\n\nLanguage:  English\nPrice:           Free of charge
  (2 training days)\nhttps://events.prace-ri.eu/event/1198/
SUMMARY:[ONLINE] Microbial community analysis with Chipster @ CSC
URL;VALUE=URI:https://events.prace-ri.eu/event/1198/
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