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33 materials found

Related resources: Input datasets  or Galaxy Server administratio... 


Statistics - Interval-Wise Testing for omics data

Statistical Analyses for omics data

Questions of the tutorial:

  • How to visualize high-resolution omics data in different groups of genomic regions?
  • How to evaluate differences in high-resolution omics data between groups of genomic regions?
  • How to detect locations and scales at which the...

Resource type: Tutorial

Assembly - Making sense of a newly assembled genome

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Genome Annotation - Genome annotation with Prokka

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...

Resource type: Tutorial

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

Variant Analysis - Mapping and molecular identification of phenotype-causing mutations

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • What is mapping-by-sequencing?
  • How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?

Objectives of the tutorial:

  • Use joint...

Resource type: Tutorial

Variant Analysis - Microbial Variant Calling

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How do we detect differences between a set of reads from a microorganism and a reference genome

Objectives of the tutorial:

  • Find variants between a reference genome and a set of...

Resource type: Tutorial

Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Questions of the tutorial:

  • Why is a Hi-C analysis useful?
  • What is...

Resource type: Tutorial

Variant Analysis - Calling variants in non-diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How does frequency of mitochondrial polymorphisms change from mother to child?

Objectives of the tutorial:

  • Using Galaxy's main site we will see how to call variants in bacteria,...

Resource type: Tutorial

Galaxy Server administration - Connecting Galaxy to a compute cluster

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • How to connect Galaxy to a compute cluster?
  • How can I configure job dependent resources, like cores, memory for my DRM?

Objectives of the tutorial:

  • Be familiar with the basics of installing,...

Resource type: Tutorial

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

Assembly - Unicycler Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Transcriptomics - Visualization of RNA-Seq results with CummeRbund

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How are RNA-Seq results stored?
  • Why are visualization techniques needed?
  • How to select our desired subjects for differential gene expression analysis?

Objectives of the tutorial:

  • Manage RNA-Seq...

Resource type: Tutorial

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

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

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

Assembly - De Bruijn Graph Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Introduction to Genome Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Introduction to Galaxy Analyses - From peaks to genes

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Questions of the tutorial:

  • How to use Galaxy?
  • How to get...

Resource type: Tutorial

Epigenetics - DNA Methylation data analysis

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Questions of the tutorial:

  • What is methylation and why it cannot be...

Resource type: Tutorial

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 - Differential abundance testing of small RNAs

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • What small RNAs are expressed?
  • What RNA features have significantly different numbers of small RNAs targeting them between two conditions?

Objectives of the tutorial:

  • Process small RNA-seq datasets...

Resource type: Tutorial

Transcriptomics - De novo transcriptome reconstruction with RNA-Seq

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • What genes are differentially expressed between G1E cells and megakaryocytes?
  • How can we generate a transcriptome de novo from RNA sequencing data?

Objectives of the tutorial:

  • Analysis of RNA...

Resource type: Tutorial

Metagenomics - Analyses of metagenomics data - The global picture

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Questions of the tutorial:

  • How to analyze metagenomics data?
  • What information can be extracted of metagenomics data?
  • What is the difference between amplicon and shotgun data?
  • What are the difference...

Resource type: Tutorial

Metagenomics - 16S Microbial Analysis with Mothur

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Questions of the tutorial:

  • What is the effect of normal variation in the gut microbiome on host health?

Objectives of the tutorial:

  • Analyze of 16S rRNA sequencing data using the Mothur toolsuite in...

Resource type: Tutorial

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 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 - 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 - Metaproteomics tutorial

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?
  • How can I perform taxonomy analysis and visualize metaproteomics data?
  • How can I perform...

Resource type: Tutorial

Sequence analysis - RAD-Seq to construct genetic maps

Analyses of sequences

Questions of the tutorial:

  • How to analyze RAD sequencing data for a genetic map study?

Objectives of the tutorial:

  • SNP calling from RAD sequencing data
  • Find and correct haplotypes
  • Create input files for genetic map building software

Resource type: Tutorial

Sequence analysis - RAD-Seq de-novo data analysis

Analyses of sequences

Questions of the tutorial:

  • How to analyze RAD sequencing data without a reference genome for a population genomics study?

Objectives of the tutorial:

  • Analysis of RAD sequencing data without a reference genome
  • SNP calling from RAD sequencing data
  • Calculate...

Resource type: Tutorial