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...

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...

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...

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.

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...

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...

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...

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,...

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...

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...

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...

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.

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...

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 -...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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.

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...

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...

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

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...

Analyses of sequences

Questions of the tutorial:

• How to analyze RAD sequencing data using a reference genome for a population genomics study?

Objectives of the tutorial:

• Analysis of RAD sequencing data using a reference genome
• SNP calling from RAD sequencing data
• Calculate population...