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NGS introduction to sequencing platforms

HTS-introduction
Quality Control

RNA-Seq FASTQ RNA-Seq Pre-processing QC
Exploratory analysis and downstream analysis

Statistical-model Exploratory-analysis
NGS introduction to file formats

HTS-introduction FASTQ BAM VCF WIG CRAM GFF3
EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014

RNA-Seq FASTQ GFF3 BAM Populus-tremula RNA-Seq Pre-processing QC Alignment Annotation …
Introduction to HTS

HTS-introduction
Lecture slides for the course RNA-seq data analysis with Chipster

FASTQ QC Pre-processing Alignment BAM Expression-estimation Feature-summarisation Differential-expression Statistical-model Exploratory-analysis
Annotation

RNA-Seq GFF3 Populus-tremula RNA-Seq Annotation
Alignment

RNA-Seq BAM Populus-tremula RNA-Seq QC Alignment
ChIP-seq analysis using R

ChIP-Seq Experimental-design QC Data-format Alignment Peak-calling Differential-binding Visualisation Annotation
Day 2 - RNA-Seq Analysis

Alignment BAM FASTA FASTQ QC Exploratory-analysis Feature-summarisation Pre-processing
RNA-seq module Frederik Coppens

RNA-Seq RNA-Seq Alignment BAM FASTQ Feature-summarisation Pre-processing QC
Introduction to NGS and RNA-seq

HTS-introduction Data-format Alignment Differential-expression Feature-summarisation QC
Data objects for R practice codes

R-programming
Day 1 - RNA-Seq Analysis

Alignment BAM FASTA FASTQ QC
Exercises for the course RNA-seq data analysis with Chipster

FASTQ QC Pre-processing Alignment BAM Expression-estimation Feature-summarisation Differential-expression Statistical-model Exploratory-analysis
Guidelines for this folder
Differential expression analysis on the Robinson, Delhomme et al. dataset.

RNA-Seq RNA-Seq Differential-expression R-programming Statistical-model
Edinburgh genomics introduction to RNA-seq data analysis
Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material

RNA-Seq FASTQ GFF3 BAM Populus-tremula RNA-Seq Pre-processing QC Alignment Annotation …
Introduction to R and Bioconductor lecture

R-programming
Populus tremula shows no evidence of sexual dimorphism

RNA-Seq FASTQ GFF3 BAM Populus-tremula RNA-Seq Pre-processing QC Alignment Annotation …
RNA-seq module Eija Korpelainen

FASTQ QC Pre-processing Alignment BAM Expression-estimation Feature-summarisation Differential-expression Statistical-model Exploratory-analysis
Differential expression analysis

Differential-expression Statistical-model
Material provided by Charlotte Soneson

RNA-Seq RNA-Seq Differential-expression Statistical-model Exploratory-analysis
RNA-Seq Analysis with Biocluster and R

RNA-Seq RNA-Seq Alignment Annotation BAM Differential-expression Exploratory-analysis Expression-estimation FASTA FASTQ …
Preprocessing RNA-Seq data

Pre-processing
Intro to R and Bioconductor

Prerequisite R-programming
Prerequisite

Statistics and probability Unix Linux R-programming Statistics
Tutorial

RNA-Seq FASTQ GFF3 BAM Populus-tremula RNA-Seq Pre-processing QC Alignment Annotation …

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