Content provider: Coursera or Galaxy Training
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...
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...
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
-...
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?
-...
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...
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...
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...
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
-...
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.
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...
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
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
-...
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
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...
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
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
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...
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...
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
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...
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...
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!
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...
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?
...