Question: Figuring out HiC restriction enzyme
1
gravatar for gbdias
7 months ago by
gbdias60
gbdias60 wrote:

Hi,

Does anyone have a strategy for figuring out which restriction enzyme was utilized in a HiC experiment based on the Illumina reads alone?

Thanks

scaffolding hic hi-c • 433 views
ADD COMMENTlink modified 3 months ago by joneill4x30 • written 7 months ago by gbdias60
3
gravatar for gbdias
7 months ago by
gbdias60
gbdias60 wrote:

Figured it out by checking the overrepresented k-mers at the FASTQC report for my data.

ADD COMMENTlink written 7 months ago by gbdias60

Can you go into further detail how you figured it out gbdias? I am in the same situation as you were. There are 20 over-represented 7-mers located near the start of my reads. (Both for forward reads and reverse reads). How do I used this data to deduce the restriction enzyme cutting site?

ADD REPLYlink written 3 months ago by joneill4x30

Check if the first 2-3 bases are common and then make a palindrome of that. For example, if the k-mers tend to start with TC then GATC is the cut site and DpnII was used.

ADD REPLYlink written 3 months ago by Devon Ryan86k
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