conversion of bedpe (customized bedpe) to .hic through pre juicer

[Adeel]

Hello mates, 

I have a bedpe file (below picture), i want to extract input data for Pre juicer to convert it into .hic format. kindly help me to extract data from following file format. 
Yes, i have already read previous discussion related to format conversion but i couldn't  find it helpful for my data.

Thanks in advance. 

[Moshe Olshansky]

Hi Adeel,

You can write a simple awk script to convert the data in your bedpe file into juicer short format and then use pre to create hic file.

Hope this helps,

Moshe.

[Samir Rahman]

I actually wanted to know the opposite. How do you convert a .hiC format into bedpe?

[Moshe Olshansky]

Hi Samir,

I do not think that you can do this exactly since hic file does not keep individual reads but rather counts for every pair of bins. You can get these counts using juicer dump for each pair of chromosomes (and then combining all of them if you need this genome-wide). Just be warned that dump ... chr1 chr7 ...  and dump ... chr7 chr1 ... produce identical results. I am not sure whether this is determined by the lexicographical order or the order in which the chromosomes appeared in the file used while creating the hic file. Would be good if "juicer people" comment on this, and if the latter also say how to infer this order from the hic file.

Best regards,

Moshe.