Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- How is raw CLIP-Seq data processed and analysed?
- How do I find binding motifs and targets for a protein (e.g., RBFOX2)?
Objectives of the tutorial:
- Remove Adapters, Barcodes and Unique Molecular...
Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/clipseq/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-clip-seq-data-analysis-from-pre-processing-to-motif-detection
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- How is raw CLIP-Seq data processed and analysed?
- How do I find binding motifs and targets for a protein (e.g., RBFOX2)?
Objectives of the tutorial:
- Remove Adapters, Barcodes and Unique Molecular Identifiers (UMIs) from the reads
- Align trimmed reads with STAR
- De-duplicate the read library
- Inspect the read mapping and de-duplication quality
- Perform peak calling with PEAKachu
- Analyse the peaks and find potential binding motifs and targets
- Check the quality of the peak calling
Florian-H-Lab
dmaticzka
bebatut
Assembly - Making sense of a newly assembled genome
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 - Making sense of a newly assembled genome
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/ecoli_comparison/tutorial.html
http://tess.elixir-uk.org/materials/assembly-making-sense-of-a-newly-assembled-genome
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 just assembled a genome. How does it compare with already sequenced genomes?
- How do I find rearranged, inserted, or deleted regions?
Objectives of the tutorial:
- Identification of the most closely related genome to my new assembly
- Perform sequence comparison to locate rearrangements
- Identify genes located in deletions
nekrut
delphine-l
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
Transcriptomics - Visualization of RNA-Seq results with CummeRbund
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- How are RNA-Seq results stored?
- Why are visualization techniques needed?
- How to select our desired subjects for differential gene expression analysis?
Objectives of the tutorial:
- Manage RNA-Seq...
Transcriptomics - Visualization of RNA-Seq results with CummeRbund
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-visualization-of-rna-seq-results-with-cummerbund
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- How are RNA-Seq results stored?
- Why are visualization techniques needed?
- How to select our desired subjects for differential gene expression analysis?
Objectives of the tutorial:
- Manage RNA-Seq results
- Extract the desired subject for differential gene expression analysis
- Visualize information
bagnacan
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
Transcriptomics - Differential abundance testing of small RNAs
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What small RNAs are expressed?
- What RNA features have significantly different numbers of small RNAs targeting them between two conditions?
Objectives of the tutorial:
- Process small RNA-seq datasets...
Transcriptomics - Differential abundance testing of small RNAs
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/srna/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-differential-abundance-testing-of-small-rnas
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What small RNAs are expressed?
- What RNA features have significantly different numbers of small RNAs targeting them between two conditions?
Objectives of the tutorial:
- Process small RNA-seq datasets to determine quality and reproducibility.
- Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets.
- Differentiate between subclasses of small RNAs based on their characteristics.
- Identify differently abundant small RNAs and their targets.
malloryfreeberg
Transcriptomics - Reference-based RNA-Seq data analysis
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What are the effects of Pasilla (PS) gene depletion on splicing events?
- How to analyze RNA sequencing data using a reference genome?
Objectives of the tutorial:
- Analysis of RNA sequencing data using...
Transcriptomics - Reference-based RNA-Seq data analysis
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-reference-based-rna-seq-data-analysis
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What are the effects of Pasilla (PS) gene depletion on splicing events?
- How to analyze RNA sequencing data using a reference genome?
Objectives of the tutorial:
- Analysis of RNA sequencing data using a reference genome
- Analysis of differentially expressed genes
- Identification of functional enrichment among differentially expressed genes
bebatut
malloryfreeberg
moheydarian
erxleben
pavanvidem
blankclemens
Transcriptomics - De novo transcriptome reconstruction with RNA-Seq
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What genes are differentially expressed between G1E cells and megakaryocytes?
- How can we generate a transcriptome de novo from RNA sequencing data?
Objectives of the tutorial:
- Analysis of RNA...
Transcriptomics - De novo transcriptome reconstruction with RNA-Seq
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/de-novo/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-de-novo-transcriptome-reconstruction-with-rna-seq
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What genes are differentially expressed between G1E cells and megakaryocytes?
- How can we generate a transcriptome de novo from RNA sequencing data?
Objectives of the tutorial:
- Analysis of RNA sequencing data using a reference genome
- Reconstruction of transcripts without reference transcriptome (de novo)
- Analysis of differentially expressed genes
malloryfreeberg
moheydarian
