ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Questions of the tutorial:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of Tal1?
- Which genes are regulated by Tal1?
Objectives of the tutorial:
- Inspect read quality with FastQC
-...
ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
http://galaxyproject.github.io/training-material/topics/chip-seq/tutorials/tal1-binding-site-identification/tutorial.html
http://tess.elixir-uk.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-t-cell-acute-lymphocytic-leukemia-protein-1-tal1
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Questions of the tutorial:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of Tal1?
- Which genes are regulated by Tal1?
Objectives of the tutorial:
- Inspect read quality with FastQC
- Perform read trimming with Trimmomatic
- Align trimmed reads with BWA
- Assess quality and reproducibility of experiments
- Identify Tal1 binding sites with MACS2
- Determine unique/common Tal1 binding sites from G1E and Megakaryocytes
- Identify unique/common Tal1 peaks occupying gene promoters
- Visually inspect Tal1 peaks with Trackster
malloryfreeberg
moheydarian
vivekbhr
joachimwolff
erxleben
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 - 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 - 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
