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Figuring out HiC restriction enzyme

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

hi-c hic scaffolding
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updated by nkmalini97 • nkmalini97 • written by gbdias gbdias

1 answer

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

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written by gbdias gbdias

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?

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written by joneill4x joneill4x

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.

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written by Devon Ryan Devon Ryan

@gbdias I have tried this approach. I have got the fastqc file reports. I get the k-mers that start with GATC or other enzyme's cut site (example:HindIII-AGCTT (A^AGCTT)) without having to generate a palindrome with the first 2-3 common bases. I was wondering if I can consider the enzyme from the k-mers which are mostly the appropriate cut sites. Is there any reference or standard with which we can be sure that the overrepresented sequences contain the k-mers of the enzyme restriction sites. I would want to know why we consider the overrepresented sequences in particular

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written by nkmalini97 • nkmalini97

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