Register training material
11 materials found

Authors: stortebecker  or Frederik Coppens @frcop 


Proteomics - Peptide and Protein ID using OpenMS tools

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Peptide and Protein ID using OpenMS tools https://tess.elixir-europe.org/materials/proteomics-peptide-and-protein-id-using-openms-tools Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.
Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can protein N-termini be enriched for LC-MS/MS? - How to analyze the LC-MS/MS data? Objectives of the tutorial: - Run an N-TAILS data analysis.

Resource type: Tutorial

Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS https://tess.elixir-europe.org/materials/proteomics-ntails Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can protein N-termini be enriched for LC-MS/MS? - How to analyze the LC-MS/MS data? Objectives of the tutorial: - Run an N-TAILS data analysis.
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are MS1 features? - How to quantify based on MS1 features? - How to map MS1 features to MS2 identifications? - How to evaluate and optimize the results? Objectives of the tutorial: - MS1 feature...

Resource type: Tutorial

Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL) https://tess.elixir-europe.org/materials/proteomics-peptide-and-protein-quantification-via-stable-isotope-labelling-sil Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are MS1 features? - How to quantify based on MS1 features? - How to map MS1 features to MS2 identifications? - How to evaluate and optimize the results? Objectives of the tutorial: - MS1 feature quantitation and mapping of quantitations to peptide and protein IDs.
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker https://tess.elixir-europe.org/materials/proteomics-peptide-and-protein-id Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.
Proteomics - Secretome Prediction

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to predict cellular protein localization based upon GO-terms? - How to combine multiple localization predictions? Objectives of the tutorial: - Predict proteins in the cellular secretome by using...

Resource type: Tutorial

Proteomics - Secretome Prediction https://tess.elixir-europe.org/materials/proteomics-secretome-prediction Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to predict cellular protein localization based upon GO-terms? - How to combine multiple localization predictions? Objectives of the tutorial: - Predict proteins in the cellular secretome by using GO-terms. - Predict proteins in the cellular secretome by using WolfPSORT. - Combine the results of both predictions.
Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method

Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are benefits and drawbacks of different quantitation methods? - How to choose which quantitation method bests suits my need? Objectives of the tutorial: - Choose your quantitation method.

Resource type: Tutorial

Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method https://tess.elixir-europe.org/materials/proteomics-label-free-versus-labelled-how-to-choose-your-quantitation-method Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are benefits and drawbacks of different quantitation methods? - How to choose which quantitation method bests suits my need? Objectives of the tutorial: - Choose your quantitation method.
Proteomics - Protein FASTA Database Handling

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to download protein FASTA databases of a certain organism? - How to download a contaminant database? - How to create a decoy database? - How to combine databases? Objectives of the tutorial: - Creation of a...

Resource type: Tutorial

Proteomics - Protein FASTA Database Handling https://tess.elixir-europe.org/materials/proteomics-protein-fasta-database-handling Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to download protein FASTA databases of a certain organism? - How to download a contaminant database? - How to create a decoy database? - How to combine databases? Objectives of the tutorial: - Creation of a protein FASTA database ready for use with database search algorithms.
Introduction to RNA-seq analysis 2014

This lecture gives an overview how to perform an RNA-seq experiment. A general RNA-seq workflow is outlined when a good quality genome sequence is available for your species.

Keywords: Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC

Introduction to RNA-seq analysis 2014 https://tess.elixir-europe.org/materials/introduction-to-rna-seq-analysis-2014 This lecture gives an overview how to perform an RNA-seq experiment. A general RNA-seq workflow is outlined when a good quality genome sequence is available for your species. Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC
RNA-seq training PSB 2013

This lecture gives an overview how to perform an RNA-seq experiment. First, the Illumina sequencing platform is briefly covered, followed by the different file formats in NGS. Next, an RNA-seq workflow is outlined, starting from the raw data up to differential expression. The recommended coverage...

Keywords: Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC

RNA-seq training PSB 2013 https://tess.elixir-europe.org/materials/rna-seq-training-psb-2013 This lecture gives an overview how to perform an RNA-seq experiment. First, the Illumina sequencing platform is briefly covered, followed by the different file formats in NGS. Next, an RNA-seq workflow is outlined, starting from the raw data up to differential expression. The recommended coverage and sequencing mode is touched upon as well as the effect on your analysis of divergence of your genotype compared to the reference. Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC
NGS introduction to file formats

This sub-module gives an overview of the most used file formats in Next Generation Sequencing analysis

Keywords: HTS-introduction, FASTQ, BAM, VCF, WIG, CRAM, GFF3

NGS introduction to file formats https://tess.elixir-europe.org/materials/ngs-introduction-to-file-formats This sub-module gives an overview of the most used file formats in Next Generation Sequencing analysis HTS-introduction, FASTQ, BAM, VCF, WIG, CRAM, GFF3
NGS introduction to sequencing platforms

This sub-module gives an overview of the most used sequencing platforms and their applications.

Keywords: HTS-introduction

NGS introduction to sequencing platforms https://tess.elixir-europe.org/materials/ngs-introduction-to-sequencing-platforms This sub-module gives an overview of the most used sequencing platforms and their applications. HTS-introduction