Change Ligation Site in hicpro-config.txt

[smped]

Hi,

Using the existing ligation site in the example template causes the following error when calling digest_genome.py.

Unable to detect offset for AAGCTAGCTT. Please, use '^' to specify the cutting position,
                   i.e A^GATCT for HindIII digestion.

This change corrects that error.

[nservant]

Hi, I think you are confusing two things ;

• The restriction (ie. cutting site) which is defined by the restriction enzyme used in the protocol (HindIII, DnpII, MboI, etc.), and usually is a motif with a precise cutting site (the famous ^)
• And the ligation site, which is the expected motif when two sequences has been ligated together.

So the goal of digest_genome.py script is to run an in silico digestion of the genome ... with the restriction site (with the ^), but not with the ligation site. Does it make sense for you ? Best

[smped]

Ah yes. My apologies.