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

Question

[Yogendra Bordiya]

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!

Answer 1

[harish]

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)

[Yogendra Bordiya]

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

Yogi

Answer 2

[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

[harish]

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.