Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
2020, Aug 08
Introduction
The HiCExplorer is available from the repository suite_hicexplorer. It is a set of tools from deeptools, dedicated towards analysis of data from the 3D conformation of the chromatin.
- Map the Hi-C reads to the reference genome
- Creation of a Hi-C matrix
- Plotting the Hi-C matrix
- Correction of Hi-C matrix
- TAD Calling
- A/B compartments computation
- pyGenomeTracks visualization
- Loop detection
References
- Joachim Wolff, Fidel Ramirez, Vivek Bhardwaj, Ekaterina Polkh, 2020 Hi-C analysis of Drosophila melanogaster cells using HiCExplorer (Galaxy Training Materials). /training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html Online; accessed Sat Aug 08 2020
- Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012