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Can I use two restriction enzymes to analyze HiC data using HiCExplorer

Hi My HiC library was prepared using two restriction enzymes. The HiCExplorere tool findRestSites seems to take only one enzyme site as input. Is there any way I can use two restriction enzymes and analyze my data using HiCExplorer.

Thank you!

hic hicexplorer arima hic multiple enzyme hic
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written by Yogendra Bordiya • Yogendra Bordiya

2 answers

I've had this same issue a while back. I ended up using genome_disgest.py from HiC-Pro to do that. (https://github.com/nservant/HiC-Pro)

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written by harish harish

Thank you Harish! I was able to generate a .bed file using digest_genome.py.

Yogi

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written by Yogendra Bordiya • Yogendra Bordiya

I was able to generate the list of restriction fragments (bed file) after genome digestion using two restriction enzymes used in Arima HiC kit. I used HiC-Pro digest_genome.py to do that (https://github.com/nservant/HiC-Pro). Arima kit uses two restriction enzymes ^GATC and G^ANTC. Since digest_genome.py does not allow for "N" in the cut sites. I used following command to get around this problem: 

digest_genome.py -r ^GATC G^AATC G^ATTC G^AGTC G^ACTC -o your_output.bed your_genome.fa

Yogi Bordiya

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written by Yogendra Bordiya • Yogendra Bordiya

Ahh, the latest update does support the ^N sites, I found about it on github.

However you will definitely need to process your files in a compatible format if you are using Juicer etc.

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written by harish harish

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