GENERAL INFO

All data analyzes have been performed with R version 4.4.0 and tested also on 4.0.5.

As for libraries version with R 4.4.0 :

crayon : 1.5.2
GenomicRanges : 1.56.0
dplyr : 1.1.4
ggplot2 : 3.5.1
data.table : 1.15.4
ggpubr : 0.6.0
karyoploteR : 1.30.0
rtracklayer : 1.64.0
corrr : 0.4.4
GGally : 2.2.1
ComplexHeatmap : 2.20.0
plyr : 1.8.9
CAinterprTools : 1.1.0
RColorBrewer : 1.1.3
ggVennDiagram : 1.5.2
ggdendro: 0.2.0

and for R 4.0.5 :

crayon : 1.5.2
GenomicRanges : 1.42.0
dplyr : 1.1.4
ggplot2 : 3.4.2
data.table : 1.15.2
ggpubr : 0.6.0
karyoploteR : 1.16.0
rtracklayer : 1.50.0
corrr : 0.4.4
GGally : 2.2.1
ComplexHeatmap : 2.20.0
plyr : 1.8.9
CAinterprTools : 1.1.0
RColorBrewer : 1.1.3
ggVennDiagram : 1.2.2
ggdendro: 0.2.0

SEQ DATA ALIGNMENTS

INIT

Download required files with src/00_init_project.sh Then use related .sh script to align raw data for each sequencing type

PREPROCESSING

Chromosomes arms

In order to generate chromsome arms bed positions use lift_over_chr_arms.R script.

Genome bed and Tiled genome bed

Those data can be obtained through tiled_genome_bed.R script

Union and intersection of peaksets

Union and intersection of peaksets can be retrieved using bedtools.sh script.

TADscore BM to BigWig

To transform .bm tad separation score files to bigwig please use bm2bw.R.

Contact matrix in .rds format

Use g2ih5_To_cm_rds.R to turn g2i.h5 matrices into .rds R format

ChIP-seq Profiles

After performing union & intersection of peakset, use computeMatrixProfile.sh script to compute ChIP-seq bigwig signal profile around peaks of interest.

ANALYZES

This repo stores bioinformatic R scripts used to generate manuscript figures. All scripts start with this line that has to be modified accordingly to the path used to clone this repo :

setwd(dir = "config/src/R/github/")

DATA PATH

FOLDER STRUCTURE

Data must be stored in /data folder along with the scripts . It must contain the following folders :

data/ChIPseq : Contains bed, bigwig and ${ip}_${condition}_newzs_prof.txt profile files.
data/RNAseq : Contains deseq2_counts_all_conditions.txt and matrecap_genes_ce11.gtf files
data/HiC : Contains all contact matrices (norm.KR.g2i.h5, obs_exp.g2i.h5, norm.KR.cm.rds, obs_exp.cm.rds), all bigwig for Eigen vectors (pca1.bw), bigwig for TAD separation scores tad_score.bw and TAD in bed format

NOTES

The following additional files must be stored in ChIPseq folder :

ce11_noMT.bed
ce11_tiled_10kb.bed
ce11_tiled_1kb.bed
ce11_tiled_25kb.bed
ce11_tiled_5kb.bed
chr_arms_ce11.bed
genes_ce11.bed

If you prefer storing them elsewhere, you will need to adapt scripts for manuscript figures accordingly.

CuvierLab/Compartments-Gen2i