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1609 materials found

Hands-on for 'Designing plasmids encoding predicted pathways by using the BASIC assembly method' tutorial

The questions this addresses are:
- How to design plasmids encoding predicted pathways using BASIC assembly method ?
- How to generate scripts enabling the automatic build of plasmids ?

The objectives are:
- Annotate the SBML pathway using Selenzy tool.
- Design plasmids encoding predicted...

Keywords: synthetic-biology

Resource type: hands-on tutorial

Hands-on for 'ATAC-Seq data analysis' tutorial

The questions this addresses are:
- Which DNA regions are accessible in the human lymphoblastoid cell line GM12878?
- How to analyse and visualise ATAC-Seq data?

The objectives are:
- Apply appropriate analysis and quality control steps for ATAC-Seq
- Generate a heatmap of transcription...

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: hands-on tutorial

Hands-on for 'Formation of the Super-Structures on the Inactive X' tutorial

The questions this addresses are:
- Histone modification?
- How is a raw set of ChIP-seq data processed and analyzed?
- Where are the enriched regions for H3K27me3, H3K4me3 and CTCF on the chrX?

The objectives are:
- Inspect the read quality
- Trim low quality bases
- Map reads on a...

Scientific topics: Epigenomics

Keywords: epigenetics, ChIP-seq

Resource type: hands-on tutorial

Hands-on for 'Hi-C analysis of Drosophila melanogaster cells using HiCExplorer' tutorial

The questions this addresses are:
- Why is a Hi-C analysis useful?
- What is 'chromosome conformation capture'?
- What are main steps in order to generate and plot a Hi-C contact matrix?

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: hands-on tutorial

Hands-on for 'DNA Methylation data analysis' tutorial

The questions this addresses are:
- What is methylation and why it cannot be recognised by a normal NGS procedure?
- Can a different methylation influence the expression of a gene? How?
- Which tools you can use to analyse methylation data?

The objectives are:
- Learn how to analyse...

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: hands-on tutorial

Hands-on for 'Identification of the binding sites of the Estrogen receptor' tutorial

The questions this addresses are:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of the Estrogen receptor?

The objectives are:
- Inspect read quality with FastQC
- Map reads with Bowtie2
- Assess the quality of an ChIP-seq experiments
- Extract coverage...

Scientific topics: Epigenomics

Keywords: epigenetics, ChIP-seq, work-in-progress

Resource type: hands-on tutorial

Hands-on for 'Infinium Human Methylation BeadChip' tutorial

The questions this addresses are:
- Which DNA regions and positions are diffrentialy methylated in pre MAPKi treatment and post MAPKi resistance Melanomas GSE65183?
- How to analyse and visualise Infinium Human Methylation BeadChip's?

The objectives are:
- Learn how to perform reproducible...

Scientific topics: Epigenomics

Keywords: epigenetics

Resource type: hands-on tutorial

Hands-on for 'Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)' tutorial

The questions this addresses are:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of TAL1?
- Which genes are regulated by TAL1?

The objectives are:
- Inspect read quality with FastQC
- Perform read trimming with Trimmomatic
- Align trimmed reads with BWA
...

Scientific topics: Epigenomics

Keywords: epigenetics, ChIP-seq

Resource type: hands-on tutorial

Hands-on for 'Genome Assembly of MRSA using Oxford Nanopore MinION Data' tutorial

The questions this addresses are:
- How to check the quality of the MinION data?
- How to perform an assembly with MinION data?
- What species do I have and what is its sequence type?
- Which resistance genes are on my genome?
- Where are the genes located on my genome?

The objectives...

Keywords: assembly, nanopore, assembly, amr

Resource type: hands-on tutorial

Hands-on for 'Chloroplast genome assembly' tutorial

The questions this addresses are:
- How can we assemble a chloroplast genome?

The objectives are:
- Assemble a chloroplast genome from long reads
- Polish the assembly with short reads
- Annotate the assembly and view
- Map reads to the assembly and view

Keywords: assembly, plants, nanopore

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 'VGP assembly pipeline' tutorial

The questions this addresses are:
- what combination of tools can produce the highest quality assembly of vertebrate genomes?
- How can we evaluate how good it is?

The objectives are:
- Learn the tools necessary to perform a de novo assembly of a vertebrate genome
- Evaluate the quality of...

Keywords: assembly, pacbio, eukaryote, VGP

Resource type: hands-on tutorial

Hands-on for 'Genome assembly using PacBio data' tutorial

The questions this addresses are:
- How to perform a genome assembly with PacBio data ?
- How to check assembly quality ?

The objectives are:
- Assemble a Genome with PacBio data
- Assess assembly quality

Keywords: assembly, assembly, pacbio

Resource type: hands-on tutorial

Hands-on for 'VGP assembly pipeline - short version' tutorial

The questions this addresses are:
- what combination of tools can produce the highest quality assembly of vertebrate genomes?
- How can we evaluate how good it is?

The objectives are:
- Learn the tools necessary to perform a de novo assembly of a vertebrate genome
- Evaluate the quality of...

Keywords: assembly, pacbio, eukaryote, VGP

Resource type: hands-on tutorial

Hands-on for 'Making sense of a newly assembled genome' tutorial

The questions this addresses are:
- I just assembled a genome. How does it compare with already sequenced genomes?
- How do I find rearranged, inserted, or deleted regions?

The objectives are:
- Identification of the most closely related genome to my new assembly
- Perform sequence...

Keywords: assembly, prokaryote

Resource type: hands-on tutorial

Hands-on for 'Unicycler Assembly' tutorial

The questions this addresses are:
- I have short reads and long reads. How do I assemble a genome?

The objectives are:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with...

Keywords: assembly, prokaryote

Resource type: hands-on tutorial

Hands-on for 'An Introduction to Genome Assembly' tutorial

The questions this addresses are:
- How do we perform a very basic genome assembly from short read data?

The objectives are:
- assemble some paired end reads using Velvet
- examine the output of the assembly.

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'Genome Assembly of MRSA using Illumina MiSeq Data' tutorial

The questions this addresses are:
- How to check the quality of the MiSeq data?
- How to perform an assembly with MiSeq data?
- What species do I have and what is its sequence type?
- Which resistance genes are on my genome?
- Where are the genes located on my genome?

The objectives are:
...

Keywords: assembly, illumina, assembly, amr

Resource type: hands-on tutorial

Hands-on for 'De Bruijn Graph Assembly' tutorial

The questions this addresses are:
- What are the factors that affect genome assembly?
- How does Genome assembly work?

The objectives are:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an assembly...

Keywords: assembly

Resource type: hands-on tutorial

Hands-on for 'GTN Metadata' tutorial

The questions this addresses are:
- What metadata is required or possible to set in a Tutorial, Slide, Topic, or FAQ

The objectives are:
- Know where to find all of the available metadata, so you can reference it later.

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Generating PDF artefacts of the website' tutorial

The questions this addresses are:
- How to generate PDF of the different tutorials and slides?

The objectives are:
- Generating PDFs

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Creating Interactive Galaxy Tours' tutorial

The questions this addresses are:
- What is a Interactive Galaxy Tour?
- How can we create an Interactive Tour?

The objectives are:
- Creating a Galaxy tour from scratch
- Deploying and running a tour

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Contributing with GitHub via command-line' tutorial

The questions this addresses are:
- How can I contribute to an open-source project with GitHub?
- What is the GitHub flow?

The objectives are:
- Fork a repository on GitHub
- Clone a remote repository locally
- Create a branch
- Commit changes
- Push changes to a remote repository
-...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Adding auto-generated video to your slides' tutorial

The questions this addresses are:
- How can we add auto-generated video?
- How does it work?
- What do I need to do to make it optimal for viewers?

The objectives are:
- Adding a video to a set of slides

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Tools, Data, and Workflows for tutorials' tutorial

The questions this addresses are:
- How can we define the technical infrastructure for a tutorial?
- How to define the tools needed for a tutorial?
- How to add the needed data directly in an instance?
- How to add the workflows related to a tutorial?
- How can we check the technical...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Creating content in Markdown' tutorial

The questions this addresses are:
- How to write a tutorial with hands-on?
- What are the different boxes?
- How can I add a caption to an image?

The objectives are:
- Create hands-on
- Use the different boxes

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Creating a new tutorial' tutorial

The questions this addresses are:
- How to integrate a new tutorial?
- How to make a tutorial robust and reproducible?

The objectives are:
- Create a tutorial from scratch
- Link a tutorial to a topic
- Create hands-on
- Add technical support for a tutorial

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Running the GTN website online using GitPod' tutorial

The questions this addresses are:
- How can I get a preview of the GTN website using GitPod?

The objectives are:
- Preview the GTN website online via GitPod
- Make changes to the GTN website and preview those changes

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Adding Quizzes to your Tutorial' tutorial

The questions this addresses are:
- How to make a quiz?

The objectives are:
- Create a quiz

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Including a new topic' tutorial

The questions this addresses are:
- How to include a new topic?

The objectives are:
- Create a new topic
- Set up the metadata for a topic

Keywords: contributing

Resource type: hands-on tutorial