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14 materials found

Authors: Malachi Griffith  or erxleben 


Informatics for RNA-Seq Analysis 2018 Module 4-Reference Free Alignment

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2018 Module 4-Reference Free Alignment http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2018-module-4-reference-free-alignment Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate Students
Informatics for RNA-Seq Analysis 2018 Module 1-Introduction to RNA Sequencing Analysis

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2018 Module 1-Introduction to RNA Sequencing Analysis http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2018-module-1-introduction-to-rna-sequencing-analysis Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Biologists, Genomicists, Computer Scientists Graduate students Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 5-Isoform Discovery and Alternative Expression

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 5-Isoform Discovery and Alternative Expression http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-5-isoform-discovery-and-alternative-expression Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 4-Reference Free Alignment

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 4-Reference Free Alignment http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-4-reference-free-alignment Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate Students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 1-Introduction to RNA Sequencing Analysis

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 1-Introduction to RNA Sequencing Analysis http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-1-introduction-to-rna-sequencing-analysis Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
High-Throughput Biology 2017 Module 11-Isoform Discovery and Alternative Expression

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 11-Isoform Discovery and Alternative Expression http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-11-isoform-discovery-and-alternative-expression Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate Students Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 10-Reference Free Alignment

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 10-Reference Free Alignment http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-10-reference-free-alignment Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 7-Introduction to RNA Sequencing Analysis

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 7-Introduction to RNA Sequencing Analysis http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-7-introduction-to-rna-sequencing-analysis Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Genome Annotation - Genome Annotation

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

Resource type: Tutorial

Genome Annotation - Genome Annotation http://tess.elixir-uk.org/materials/genome-annotation-genome-annotation Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
ChIP-Seq data analysis - Identification of the binding sites of the Estrogen receptor

ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of the Estrogen receptor? Objectives of the tutorial: - Inspect read quality with FastQC - Map reads with...

Resource type: Tutorial

ChIP-Seq data analysis - Identification of the binding sites of the Estrogen receptor http://tess.elixir-uk.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-estrogen-receptor ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of the Estrogen receptor? Objectives of the tutorial: - Inspect read quality with FastQC - Map reads with Bowtie2 - Assess the quality of an ChIP-seq experiments - Extract coverage files - Call enriched regions or peaks
Variant Analysis - Exome sequencing data analysis

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to identify the genetic variation with the use of exome sequencing? - What is the pipeline of the process of finding genetic variation which caused the disease? Objectives of the...

Resource type: Tutorial

Variant Analysis - Exome sequencing data analysis http://tess.elixir-uk.org/materials/variant-analysis-exome-sequencing-data-analysis Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to identify the genetic variation with the use of exome sequencing? - What is the pipeline of the process of finding genetic variation which caused the disease? Objectives of the tutorial: - Identification of the genetic variation using the exome sequencing - Using FreeBayes calls for variants generating - Variant analysis and GEMINI queries
ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? Objectives of the tutorial: - Inspect read quality with FastQC -...

Resource type: Tutorial

ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) http://tess.elixir-uk.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-t-cell-acute-lymphocytic-leukemia-protein-1-tal1 ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? Objectives of the tutorial: - Inspect read quality with FastQC - Perform read trimming with Trimmomatic - Align trimmed reads with BWA - Assess quality and reproducibility of experiments - Identify Tal1 binding sites with MACS2 - Determine unique/common Tal1 binding sites from G1E and Megakaryocytes - Identify unique/common Tal1 peaks occupying gene promoters - Visually inspect Tal1 peaks with Trackster
Transcriptomics - Reference-based RNA-Seq data analysis

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What are the effects of Pasilla (PS) gene depletion on splicing events? - How to analyze RNA sequencing data using a reference genome? Objectives of the tutorial: - Analysis of RNA sequencing data using...

Resource type: Tutorial

Transcriptomics - Reference-based RNA-Seq data analysis http://tess.elixir-uk.org/materials/transcriptomics-reference-based-rna-seq-data-analysis Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What are the effects of Pasilla (PS) gene depletion on splicing events? - How to analyze RNA sequencing data using a reference genome? Objectives of the tutorial: - Analysis of RNA sequencing data using a reference genome - Analysis of differentially expressed genes - Identification of functional enrichment among differentially expressed genes
Transcriptomics - Introduction to Transcriptomics

Training material for all kinds of transcriptomics analysis.

Transcriptomics - Introduction to Transcriptomics http://tess.elixir-uk.org/materials/transcriptomics-introduction Training material for all kinds of transcriptomics analysis.