epigenomics-data-descriptor

Scripts to call super enhancers, filter and generate ChIP-seq heatmaps for neuroblastoma epigenomics data descriptor paper, and to calculate IDR.

Table of Contents

• 1. LILY (Super Enhancer calling)
• 2. ChipSeq Heatmaps
• 3. IDR Analysis
• Additional info

1. LILY (Super Enhancer calling)

LILY is a pipeline for detection of super-enhancers using H3K27ac ChIP-seq data, which includes explicit correction for copy number variation inherent to cancer samples. The pipeline is based on the ROSE algorithm originally developed by the the Young lab.

Before running

Follow steps 1-3 provided in the LILY's github documentation (https://github.com/BoevaLab/LILY). Clone the repository to run LILY scripts.

Prerequisites

You will need following files to run LILY:

1. narrowPeak, regions.bed and .wig files for a particular sample should be present in the data folder
2. hg19_refseq.ucsc (transcriptome information which can be found at https://github.com/linlabbcm/rose2/tree/master/rose2/annotation)
3. hg19.chrom.sizes (file with chromosome lengths)

How to run

Script calls super enhances iteratively for all lines. Make sure to change data directory and result directory paths before running the script.

Rscript lily.R

2. ChipSeq Heatmaps

ChipSeq heatmaps were generated for MYCN (annotating top 5K peaks present in at least 5 mycn amplified cell lines) and all histone marks for COGN415 and NB69 line (annotating promoters, enhancers and super enhancers called from step 1)

Prerequisites

deepTools 3.2.0

How to run

• To generate MYCN heatmaps (with top 5K peaks)

Rscript makeHeatmaps.R

To generate heatmaps of histone-marks for COGN415 and NB69:

• To plot promoters

Rscript promoterPlot.R

• To plot enhancers

Rscript enhancerPlot.R

• To plot Super Enhancers

Rscript SEPlot.R

3. IDR Analysis

The number of peaks passing the IDR threshold is calculated between true replicates (Nt), pooled pseudoreplicates (Np), self-pseudoreplicates1 (N1) and self-pseudoreplicates2 (N2).

• Nt: iqr_selfreps_noinput_merged_Final.sh
• Np: shuffle_bam_pooled_pseudoreps_noinput_Final.sh
• N1: shuffle_bam_pseudo_selfreps_noinput_REP1_Final.sh
• N2: shuffle_bam_pseudo_selfreps_noinput_REP2_Final.sh

Example run

qsub iqr_selfreps_noinput.sh Cell_REP1 Cell_REP2 Cell_Merged_Self_IDR

Additional info

Authors: Khushbu Patel (@kpatel427), Apexa Modi (@apexamodi), Jo Lynne Rokita (@jharenza)

Organization: The Children's Hospital of Philadelphia (CHOP)