https://github.com/neurogenomics/tf-analysis-cuttag

nanoCUT&TAG analysis of 17 transcription factors (TFs) in K562 human cells
https://github.com/neurogenomics/tf-analysis-cuttag

epigenomics motif-enrichment-analysis r-analysis

Last synced: 3 months ago
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nanoCUT&TAG analysis of 17 transcription factors (TFs) in K562 human cells

• Host: GitHub
• URL: https://github.com/neurogenomics/tf-analysis-cuttag
• Owner: neurogenomics
• License: mit
• Created: 2025-05-13T13:15:52.000Z (5 months ago)
• Default Branch: master
• Last Pushed: 2025-06-11T11:01:11.000Z (4 months ago)
• Last Synced: 2025-06-11T12:21:55.624Z (4 months ago)
• Topics: epigenomics, motif-enrichment-analysis, r-analysis
• Language: R
• Homepage:
• Size: 17.6 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          

# nanoCUT&Tag - 17TFs - K562 cells - Analysis

**README Last Updated:** May 2025

## Authors

- **Experiment:** Isidora Gocmanac

- **Scripts:** Hiranyamaya (Hiru) Dash

This project is part of Isidora's PhD.

## Notes

- **Alignment data source:** Imperial HPC `/rds/general/user/$USER/projects/neurogenomics-lab/live/Data/cutandtag/processed_data/cuttag_18_04_2025_Isidora`

- **5'-shift peak calling method used for CUT&Tag:** [biorxiv - Rational design of peak calling parameters for TIP-seq based on pA-Tn5 insertion patterns improves predictive power](https://www.biorxiv.org/content/10.1101/2024.10.08.617149v1) 

- Default settings with control files were used for Chip-seq peak calling.  

- **Motif analysis:** [MotifPeeker R Package](https://github.com/neurogenomics/MotifPeeker)

- For our analysis, we use ChIP-seq peak files from ENCODE,

`01_peakcall_chipseq.R` was NOT used.