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