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14 materials found

Authors: Obi Griffith  or Bernardo Clavijo  or erxleben 


Informatics for RNA-Seq Analysis 2018 Module 3-Expression and Differential 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 2018 Module 3-Expression and Differential Expression https://tess.elixir-europe.org/materials/informatics-for-rna-seq-analysis-2018-module-3-expression-and-differential-expression 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 3-Expression and Differential 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 3-Expression and Differential Expression https://tess.elixir-europe.org/materials/informatics-for-rna-seq-analysis-2017-module-3-expression-and-differential-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
High-Throughput Biology 2017 Module 9-Expression and Differential 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 9-Expression and Differential Expression https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-9-expression-and-differential-expression Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Post-Doctoral Fellows Researchers Biologists, Genomicists, Computer Scientists
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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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) https://tess.elixir-europe.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 - Introduction to Transcriptomics

Training material for all kinds of transcriptomics analysis.

Transcriptomics - Introduction to Transcriptomics https://tess.elixir-europe.org/materials/transcriptomics-introduction Training material for all kinds of transcriptomics analysis.
Genome assembly and validation

Course materials from the 2015 de novo course.

Keywords: Earlham Institute

Genome assembly and validation https://tess.elixir-europe.org/materials/genome-assembly-and-validation Course materials from the 2015 de novo course. Earlham Institute
Data QC and preparation

Course materials from the data QC and preparation course.

Keywords: Earlham Institute

Data QC and preparation https://tess.elixir-europe.org/materials/data-qc-and-preparation Course materials from the data QC and preparation course. Earlham Institute
A simple genome assembly

Course materials from the 2015 De Novo course.

Keywords: Earlham Institute

A simple genome assembly https://tess.elixir-europe.org/materials/a-simple-genome-assembly Course materials from the 2015 De Novo course. Earlham Institute
First pass assembly and QC

Course materials from the 2015 De Novo course.

Keywords: Earlham Institute

First pass assembly and QC https://tess.elixir-europe.org/materials/first-pass-assembly-and-qc Course materials from the 2015 De Novo course. Earlham Institute
Sequencing Technologies

Course materials from the 2015 de novo course.

Scientific topics: Sequencing

Keywords: De Novo, Earlham Institute

Sequencing Technologies https://tess.elixir-europe.org/materials/sequencing-technologies Course materials from the 2015 de novo course. Sequencing De Novo, Earlham Institute
SeqAhead: NGS current challenges and data analysis for plant researchers

Complete course materials from the 2014 NGS course.

Keywords: next generation sequencing, Earlham Institute

SeqAhead: NGS current challenges and data analysis for plant researchers https://tess.elixir-europe.org/materials/seqahead-ngs-current-challenges-and-data-analysis-for-plant-researchers Complete course materials from the 2014 NGS course. next generation sequencing, Earlham Institute