Galaxy Spring day 2019
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Pretreatments
Data upload
Quality control
Outline and general concepts for the RNAseq analysis
RNAseq librairies - cDNA synthesis
RNAseq librairies - Inserts and sequencing strategies
The key idea in Reference-base Expression analysis
Reflecting on quality control & “filtering” in RNAseq analysis
Transcript Quantification
Statistical Analysis of Differential expression
Experimental procedures affect downstream analyses
Quality filtering
Optional filtering of reads on sequence quality
Mapping
Mapping
Mapping the reads to the reference genome
RNA STAR
HiSAT2
BAM inspection
Visualisation of read mapping
Analysis of the differential gene expression
Introduction to read counting
Estimation of the strandness
Count the number of reads per annotated gene
Identification of the differentially expressed features - DESeq2
DESeq2 use
Volcano Plot
Visualization of the differentially expressed genes
Analysis of functional enrichment among the differentially expressed genes
Introduction
GO
Galaxy Workflows
Introduction
Example
Galaxy Spring day 2019
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Mapping
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Mapping the reads to the reference genome
GitHub
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