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445 materials found

Content provider: ELIXIR Luxembourg  or Galaxy Training 


Hands-on for 'From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis' tutorial

The questions this addresses are:
- Learn how to get and use data from the Sequence Read Archive in Galaxy.

\nThe objectives are:
- Understand how Galaxy and the Sequence Read Archive interact.
- Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to...

Scientific topics: Genetic variation

Keywords: variant-analysis, covid19

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?

\nThe 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?

\nThe 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 '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 '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?

\nThe 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 '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?

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

Scientific topics: Genetic variation

Keywords: variant-analysis, cancer, cyoa

Resource type: hands-on tutorial

Hands-on for 'M. tuberculosis Variant Analysis' tutorial

The questions this addresses are:
- How do we detect differences between a set of reads from M. tuberculosis (Mtb) and the Mtb reference genome

\nThe objectives are:
- How should we filter those variants
- How can we predict drug resistance from those variants
- How do we annotate those...

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Microbial Variant Calling' tutorial

The questions this addresses are:
- How do we detect differences between a set of reads from a microorganism and a reference genome

\nThe objectives are:
- Find variants between a reference genome and a set of reads
- Visualise the SNP in context of the reads aligned to the genome
-...

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Calling variants in non-diploid systems' tutorial

The questions this addresses are:
- How does frequency of mitochondrial polymorphisms change from mother to child?

\nThe objectives are:
- Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.

Scientific topics: Genetic variation

Keywords: variant-analysis, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Calling very rare variants' tutorial

The questions this addresses are:
- What frequency of variants is so low that it is obscured by sequencing error rate?
- What are the different types of consensus sequences produced from duplex sequencing?

\nThe objectives are:
- Processing raw duplex sequencing data into consensus...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Calling variants in diploid systems' tutorial

The questions this addresses are:
- How to find variable sites in diploid genomes?

\nThe objectives are:
- Identification of genetic variations using variant calling

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Genomic Data Visualisation with JBrowse' tutorial

The questions this addresses are:
- How can I visualise features or blast data?
- How can I visualise sequencing data in a workflow

\nThe objectives are:
- Build several visualisations in JBrowse
- Have basic familiarity with moving around JBrowse, and loading several data tracks

Keywords: visualisation

Resource type: hands-on tutorial

Hands-on for 'From small to large-scale genome comparison' tutorial

The questions this addresses are:
- How can we run pairwise genome comparisons using Galaxy?
- How can we run massive chromosome comparisons in Galaxy?
- How can we quickly visualize genome comparisons in Galaxy?

\nThe objectives are:
- Learn the basics of pairwise sequence comparison
-...

Keywords: genome-annotation

Resource type: hands-on tutorial

Hands-on for 'Visualisation with Circos' tutorial

The questions this addresses are:
- What can the Circos Galaxy tool be used for?
- How can I visualise common genomic datasets using Circos?

\nThe objectives are:
- Create a number of Circos plots using the Galaxy tool
- Familiarise yourself with the various different track types

Keywords: visualisation

Resource type: hands-on tutorial

Hands-on for 'Essential genes detection with Transposon insertion sequencing' tutorial

The questions this addresses are:
- What is Transposon insertion Sequencing?
- How to get TA sites Coverage ?
- How to predict essential genes ?

\nThe objectives are:
- Understand the read structure of TnSeq analyses
- Predict Essential genes with Transit
- Compare gene essentiality in...

Keywords: genome-annotation, bacteria, tnseq, essential genes

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Maker' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome?
- How to evaluate and visualize annotated genomic features?

\nThe objectives are:
- Load genome into Galaxy
- Annotate genome with Maker
- Evaluate annotation quality with BUSCO
- View annotations in JBrowse

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Functional annotation of protein sequences' tutorial

The questions this addresses are:
- How to perform functional annotation on protein sequences?

\nThe objectives are:
- Perform functional annotation using EggNOG-mapper and InterProScan

Keywords: genome-annotation, eukaryote, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Refining Genome Annotations with Apollo' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Maker (short)' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome?
- How to evaluate and visualize annotated genomic features?

\nThe objectives are:
- Load genome into Galaxy
- Annotate genome with Maker
- Evaluate annotation quality with BUSCO
- View annotations in JBrowse

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'CRISPR screen analysis' tutorial

The questions this addresses are:
- What are the steps to process CRISPR screen data?
- How to identify essential genes across experimental conditions?

\nThe objectives are:
- Apply appropriate analysis and quality control steps for CRISPR screen data
- Identify differentially enriched...

Keywords: genome-annotation, genome editing, CRISPR, essential genes, cell line

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Prokka' tutorial

The questions this addresses are:
- How can we annotate a bacterial genome?
- How can we visualize annotated genomic features?

\nThe objectives are:
- Load genome into Galaxy
- Annotate genome with Prokka
- View annotations in JBrowse

Keywords: genome-annotation, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Masking repeats with RepeatMasker' tutorial

The questions this addresses are:
- How to mask repeats in a genome?
- What is the difference between hard and soft masking?

\nThe objectives are:
- Use RepeatMasker to soft mask a newly assmbled genome

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Set up a Galaxy for Training' tutorial

The questions this addresses are:
- How do I prepare my Galaxy instance to support a training module?
- How can I generate a Docker Galaxy instance for my topic?

\nThe objectives are:
- Use ephemeris to install the training requirements to a Galaxy instance
- Create a docker image for a...

Keywords: instructors

Resource type: hands-on tutorial

Hands-on for 'Genome annotation with Funannotate' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome with Funannotate?
- How to perform functional annotation?
- How to evaluate and visualize annotated genomic features?
- How to format the annotation for submission at NCBI?

\nThe objectives are:
- Load genome into...

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Galaxy Admin Training' tutorial

The questions this addresses are:
- How do I organise a Galaxy Admin Training (GAT)
- What do I need to set up?
- What should I know during the training?

\nThe objectives are:
- Interact with the UseGalaxy.eu admins to arrange for infrastructure
- Run a great training!

Keywords: instructors

Resource type: hands-on tutorial

Hands-on for 'Organizing a workshop' tutorial

The questions this addresses are:
- What should we think about when we organize a workshop?
- Have we done everything necessary for organising a great workshop?

Keywords: instructors

Resource type: hands-on tutorial

Hands-on for 'Training Infrastructure as a Service' tutorial

The questions this addresses are:
- Is this service appropriate for my event?

\nThe objectives are:
- Identify if it is appropriate
- Interact with the service administrators to arrange for infrastructure

Keywords: instructors, cyoa

Resource type: hands-on tutorial

Hands-on for 'Scripting Galaxy using the API and BioBlend' tutorial

The questions this addresses are:
- What is a REST API?
- How to interact with Galaxy programmatically?
- Why and when should I use BioBlend?

\nThe objectives are:
- Interact with Galaxy via BioBlend.

Keywords: dev, jupyter-notebook

Resource type: hands-on tutorial

Hands-on for 'Debugging Galaxy' tutorial

The questions this addresses are:
- How do I debug Galaxy?

\nThe objectives are:
- Fix a broken branch
- Interpret the results of failed tests on GitHub
- Run individual tests locally
- Fix errors identified by failing tests
- Debug simple runtime errors using the Python debugger
- Write...

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Creating Galaxy tools from Conda Through Deployment' tutorial

The questions this addresses are:
- How do you create a conda package used as a dependency in a Galaxy tool wrapper?
- How do you create a Galaxy tool wrapper and all of its requirements?
- How do you test a Galaxy tool wrapper after it's written?
- How do you deploy a Galaxy tool wrapper?
...

Keywords: dev

Resource type: hands-on tutorial