My script to run hicexplorer

Environment configuration

I recommend Using conda to build your analysis env.

conda create -n hicexplorer
conda activate hicexplorer
conda install hicexplorer seqkit bwa bwa-meme

How to use?

1. Config your own enzyme file. Put your Hi-C genereate enzymes in the file called enzyme.txt

Like: enzyme.txt

GATC
GA.TC
CT.AG
TTAA

2. Copy or soft link your Hi-C raw data to your current working directory.

3. Using vim open the automate_hicexplorer.sh file and change the config parameters.

To-do list:

1. Improve the if judging condition
2. Improve the pipeline consistency
3. Add more error alerts and hints.