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6 materials found

Related resources: Introduction to Galaxy dataset  or Transcriptomics dataset 


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...

Resource type: Tutorial

Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection 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
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...

Resource type: Tutorial

Transcriptomics - Visualization of RNA-Seq results with CummeRbund 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
Introduction to Galaxy Analyses - From peaks to genes

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to use Galaxy? - How to get...

Resource type: Tutorial

Introduction to Galaxy Analyses - From peaks to genes http://tess.elixir-uk.org/materials/galaxy-introduction-from-peaks-to-genes Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to use Galaxy? - How to get from peak regions to a list of gene names? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
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...

Resource type: Tutorial

Transcriptomics - Reference-based RNA-Seq data analysis 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
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...

Resource type: Tutorial

Transcriptomics - Differential abundance testing of small RNAs 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.
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...

Resource type: Tutorial

Transcriptomics - De novo transcriptome reconstruction with RNA-Seq 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