Assembly - Unicycler Assembly
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...
Assembly - Unicycler Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html
http://tess.elixir-uk.org/materials/assembly-unicycler-assembly
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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- I have short reads and long reads. How do I assemble a genome?
Objectives of the tutorial:
- 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 Prokka
nekrut
delphine-l
slugger70
Proteomics - Peptide and Protein ID using OpenMS tools
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.
Proteomics - Peptide and Protein ID using OpenMS tools
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-oms/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-id-using-openms-tools
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.
stortebecker
bgruening
Assembly - De Bruijn Graph Assembly
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...
Assembly - De Bruijn Graph Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html
http://tess.elixir-uk.org/materials/assembly-de-bruijn-graph-assembly
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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- What are the factors that affect genome assembly?
- How does Genome assembly work?
Objectives of the tutorial:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an assembly using the SPAdes assembler.
slugger70
Assembly - Introduction to Genome Assembly
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...
Assembly - Introduction to Genome Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/general-introduction/tutorial.html
http://tess.elixir-uk.org/materials/assembly-introduction-to-genome-assembly
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 Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- How do we perform a very basic genome assembly from short read data?
Objectives of the tutorial:
- assemble some paired end reads using Velvet
- examine the output of the assembly.
slugger70
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
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...
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-quant-sil/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-quantification-via-stable-isotope-labelling-sil
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 quantitation and mapping of quantitations to peptide and protein IDs.
stortebecker
bgruening
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker
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.
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-id
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.
stortebecker
bgruening
Proteomics - Secretome Prediction
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...
Proteomics - Secretome Prediction
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/secretome-prediction/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-secretome-prediction
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 GO-terms.
- Predict proteins in the cellular secretome by using WolfPSORT.
- Combine the results of both predictions.
stortebecker
bgruening
Proteomics - Metaproteomics tutorial
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...
Proteomics - Metaproteomics tutorial
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/metaproteomics/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-metaproteomics-tutorial
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 functional analysis on this metaproteomics data?
Objectives of the tutorial:
- A taxonomy and functional analysis of metaproteomic mass spectrometry data.
timothygriffin
pratikdjagtap
jj-umn
blankclemens
