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

Resource type: Tutorial

Authors: Florian-H-Lab, dmaticzka, bebatut

External resources:
Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection https://tess.elixir-europe.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