HisTrader

Introduction

HisTrader is a tool designed to identify Nucleosome-Free Regions (NFRs) from ChIP-Seq data targeting histone modifications. It takes a signal file (bedGraph or bigWig) and a broad peak file as input, and outputs BED files identifying NFRs and nucleosome-occupied regions (NORs) within those peaks.

NFRs are detected using a combination of moving averages and second-order differencing to identify valley-like patterns within peaks.

For more details, please refer to our publication: https://doi.org/10.1016/j.crmeth.2026.101607

Installation

Requires Python 3.8+ and the following packages:

pip install histrader

# or

pip install numpy pandas pyranges pyBigWig pytest
pip install .

Usage

python histrader.py --signal ChIP.bedGraph/bigWig --peaks ChIP.bed

Required Parameters

Optional Parameters

Output Files

Example

python histrader.py \
  --signal  ChIP.bedGraph \
  --peaks   ChIP.bed \
  --method  BOTH \
  --step    25 \
  --nucSize 150 \
  --pMax    0.1 \
  --out     output_prefix

Test Data

Test data for a single H3K27ac peak on chr11 is provided in TEST_DATA/:

python histrader.py \
  --signal TEST_DATA/test.region.histrader.chr11_12286115_12289133.H3K27AC.bdg \
  --peaks  TEST_DATA/test.region.histrader.chr11_12286115_12289133.H3K27AC.broadPeak \
  --out    test_output

Tests

pytest test_histrader.py -v

Citation

If you use HisTrader in your research, please cite:

HisTrader: A Tool to Identify Nucleosome Free Regions from ChIP-Seq of Histone Post-Translational Modifications Eftyhios Kirbizakis, Yifei Yan, Ansley Gnanapragasam, Juliana Cavalcante de Moura, Xiaoyang Zhang, and Swneke D. Bailey Cell Reports Methods, 2026, 101607 https://doi.org/10.1016/j.crmeth.2026.101607