nanoCUT&Tag - 17TFs - K562 cells - Analysis

README Last Updated: May 2025

Authors

This project is part of Isidora's PhD.

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
Default settings with control files were used for Chip-seq peak calling.
Motif analysis: MotifPeeker R Package
For our analysis, we use ChIP-seq peak files from ENCODE, 01_peakcall_chipseq.R was NOT used.

Name		Name	Last commit message	Last commit date
Latest commit History 16 Commits
data		data
utils		utils
.gitignore		.gitignore
00_install_packages.R		00_install_packages.R
01_filter_read1s.sh		01_filter_read1s.sh
01_peakcall_chipseq.R		01_peakcall_chipseq.R
01_peakcall_cuttag.R		01_peakcall_cuttag.R
02_motifpeeker.R		02_motifpeeker.R
03_epicompare.R		03_epicompare.R
04_peakqval_motif.R		04_peakqval_motif.R
LICENSE		LICENSE
README.md		README.md