Register training material
14 materials found

Authors: Jan Slifka  or Wolfgang Maier 


Hands-on for 'Avian influenza viral strain analysis from gene segment sequencing data' tutorial

The questions this addresses are:
- With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?
- Is it possible to reuse existing...

Scientific topics: Genetic variation

Keywords: variant-analysis, virology, public health, work-in-progress

Resource type: hands-on tutorial

Hands-on for 'Somatic Variant Discovery from WES Data Using Control-FREEC' tutorial

The questions this addresses are:
- What are the specific challenges in locating human Copy Number Variances (hCNVs)?
- How to preprocess the sequenced reads for hCNVs detection?
- How can you detect the hCNVs in/from tumor and normal tissue of the same individual?
- How can you visualise...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Exome sequencing data analysis for diagnosing a genetic disease' tutorial

The questions this addresses are:
- How do you identify genetic variants in samples based on exome sequencing data?
- How do you, among the set of detected variants, identify candidate causative variants for a given phenotype/disease?

The objectives are:
- Jointly call variants and...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Mapping and molecular identification of phenotype-causing mutations' tutorial

The questions this addresses are:
- What is mapping-by-sequencing?
- How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?

The objectives are:
- Use joint variant calling and extraction to facilitate variant comparison across samples
-...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data' tutorial

The questions this addresses are:
- How can we extract annotated allelic variants in SARS-Cov-2 sequences in Galaxy?
- Which tools and workflows can we use to identify SARS-CoV-2 lineages in Galaxy?

The objectives are:
- Repeat SARS-CoV-2 data preparation
- Select and run workflow to...

Scientific topics: Genetic variation

Keywords: variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'Identification of somatic and germline variants from tumor and normal sample pairs' tutorial

The questions this addresses are:
- What are the specific challenges in somatic variant calling that set it apart from regular diploid variant calling?
- How can you call variants and classify them according to their presence/absence in/from tumor and normal tissue of the same individual?
-...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Trio Analysis using Synthetic Datasets from RD-Connect GPAP' tutorial

The questions this addresses are:
- How do you import data from the EGA?
- How to download files with HTSGET in Galaxy?
- How do you pre-process VCFs?
- How do you identify causative variants?

The objectives are:
- Requesting DAC access and importing data from the EGA.
- Pre-process VCFs...

Scientific topics: Genetic variation

Keywords: variant-analysis, cancer, cyoa

Resource type: hands-on tutorial

Hands-on for 'Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads' tutorial

The questions this addresses are:
- How can a genome of interest be assembled against a background of contaminating reads from other genomes?
- How can sequencing data from public sources be turned into assembly-ready polished datasets?

The objectives are:
- Obtain viral (SARS-CoV-2)...

Keywords: assembly, covid19

Resource type: hands-on tutorial

Hands-on for 'Pre-processing of Single-Cell RNA Data' tutorial

The questions this addresses are:
- What is single-cell?
- How do we process a batch?
- How do we process multiple batches?
- How do we check for cross-contamination?

The objectives are:
- Demultiplex FASTQ data via UMI-tools
- Understand and validate the extraction of barcodes
- Obtain...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell

Resource type: hands-on tutorial

Hands-on for 'Automating Galaxy workflows using the command line' tutorial

The questions this addresses are:
- How can I schedule and run tens or hundreds of Galaxy workflows easily?
- How can I automate my analyses when large amounts of data are being produced daily?

The objectives are:
- Learn to use the planemo run subcommand to run workflows from the command...

Keywords: galaxy-interface, workflows, variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'Removal of human reads from SARS-CoV-2 sequencing data' tutorial

The questions this addresses are:
- How can you remove traces of human sequence data from a sequenced viral sample?

The objectives are:
- Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources
- Organize the data into a collection
- Preprocess and map...

Keywords: sequence-analysis, covid19

Resource type: hands-on tutorial

DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data management, Data governance

Keywords: Data managment plan, data stewardship, data management, software tools

Resource type: Video, Slides, Webinar

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data governance, Data management

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides