search

nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
Other
382 stars 183 forks source link

Ligation site in configuration file #477

Open think-o opened 3 years ago

think-o commented 3 years ago

Hello!

I wanted to know how the ligation site is to be given in the configuration file. I suppose for HindIII since the cut site is A^AGCTT the reverse complement AAGCT is added to the 5' end of it. So the ligation site is AAGCTAGCTT as mentioned in the config file by default. Can I do the same with the other enzymes by generating a reverse complement and add it to the 5' end to make it a ligation site.

nservant commented 3 years ago

Hi, Yes in theory, but it might change according to the restriction enzyme and the overhang. Which enzyme did you use ? N

think-o commented 3 years ago

Hi, Yes in theory, but it might change according to the restriction enzyme and the overhang. Which enzyme did you use ? N

Thanks for the response @nservant . I have a few HiC-data sets for the enzyme Bglii and some other for DpnII. There are some for HindIII which I have run with default parameters as present in the config file

nservant commented 3 years ago

ok so for DpnII, the restriction motif if ^GATC and the ligation motif GATCGATC And for Bglii, the restriction motif is A^GATCT and the ligation should be AGATCGATCT Do you agree ? N

think-o commented 3 years ago

Yeah. I was just wondering why the first base of the restriction motif is neglected while generating the ligation motif here