Translocation-detection using Hi-C

Introduction

This script is based on the chromatin interaction clustering to detect inter-chromosomal translocations in cancer Hi-C data up to 1kb resolution. (co-developer Hao Jiang) For complete information please read (https://www.frontiersin.org/articles/10.3389/fcell.2021.706375/full)

The script requires the following dependencies:

1.   python (≥ 2.7)
   
2.   matplotlib (≥ 2.3.1)
   
3.   scipy (≥ 0.5.1)
   
4.   numpy ( ≥ 1.18)
   
5.   java ( ≥ 1.8.0_91)
   

Usage

java in-house_script.jar -bd  -f -l -minc  -minl -ml  -o  -p  -pv  s -sort -t 

 -bd           min breakpoint distance, if two breakpoints distance less than this value, it will be merged (defalut 100k) 
 -f,--bedpe    Interaction bedpe file 
 -l            extend length (defalut 10k) 
 -minc         min cluster count (default 70)
 -minl         min region distance (default 5k) 
 -ml           cluster merge length (defalut 1M) 
 -o,--out      output path 
 -p,--prefix   output prefix 
 -pv           P-value (default 5e-5) 
 -s            chr size file  
 -sort         if your input file don't sort before, add this argument 
 -t,--thread   threads  

Example

java -jar in_house_script.jar -f input.bedpe -p test_out -s chr.size -t 1 -l 20000
bedpe: Hi-C file 6 column

---

 CopyRight © 2021 Guoliang's Lab, All Rights Reserved