Codes for restriction sites of mixed restriction enzymes

[bcbanderson]

Hey, I have a HiC data for which a cocktail of mixed restriction enzymes was used for cut at the following recognition sites: ^GATC, G^ANTC, C^TNAG, and T^TAA. How to code these patterns in the section "Set ligation junction based on restriction enzyme" in juicer pipeline? Thank you!

Set ligation junction based on restriction enzyme

case $site in HindIII) ligation="AAGCTAGCTT";; DpnII) ligation="GATCGATC";; MboI) ligation="GATCGATC";; NcoI) ligation="CCATGCATGG";; none) ligation="XXXX";; *) ligation="XXXX" echo "$site not listed as recognized enzyme. Using $site_file as site file" echo "Ligation junction is undefined" exit 100 esac

[edfajardo]

You can add a line similar to the existing line for the Arima cocktail, but you would have to add the extra possible junctions yourself. The relevant Arima line is

        Arima) ligation="'(GAATAATC|GAATACTC|GAATAGTC|GAATATTC|GAATGATC|GACTAATC|GACTACTC|GACTAGTC|GACTATTC|GACTGATC|GAGTAATC|GAGTACTC|GAGTAGTC|GAGTATTC|GAGTGATC|GATCAATC|GATCACTC|GATCAGTC|GATCATTC|GATCGATC|GATTAATC|GATTACTC|GATTAGTC|GATTATTC|GATTGATC)'" ;;

That is already 25 possible junctions, coming from ^GATC, G^ANTC (two of the patterns in your cocktail). The 25 junctions arise because you have 5 cutting sequences (substituting for N in the second general pattern), and all ligations are possible: 5x5=25. To these you would have to add the possible junctions of the other cutters, C^TNAG and T^TAA, which give you an additional 5 cutting patterns for a total of 10 cutting sequence patterns. This means, if I am correct, that you have 10x10=100 possible junctions. You have some work to do here, but the syntax is as indicated (each possible ligation separated by a | symbol):

You can name this 100-sequence ligation pattern "myCocktail" or whatever you want, and then address it as such when you run juicer.sh, with the -s switch

myCocktail) ligation="'(xxxx|xxxx|your 100 ligation junctions...)'"

notice the double quote followed (or preceded) by a single quote at the start (or end).

I recommend that you read the following thread: https://groups.google.com/g/3d-genomics/c/1kgiGvi7vg8

[nchernia]

This is correct; also note that one should appropriately account for the baseline rate, which will be quite high with so many possible sequences.

On Fri, Aug 20, 2021 at 4:42 PM edfajardo @.***> wrote:

You can add a line similar to the existing line for the Arima cocktail, but you would have to add the extra possible junctions yourself. The relevant Arima line is

    Arima) ligation="'(GAATAATC|GAATACTC|GAATAGTC|GAATATTC|GAATGATC|GACTAATC|GACTACTC|GACTAGTC|GACTATTC|GACTGATC|GAGTAATC|GAGTACTC|GAGTAGTC|GAGTATTC|GAGTGATC|GATCAATC|GATCACTC|GATCAGTC|GATCATTC|GATCGATC|GATTAATC|GATTACTC|GATTAGTC|GATTATTC|GATTGATC)'" ;;

That is already 25 possible junctions, coming from ^GATC, G^ANT (two of the patterns in your cocktail). The 25 junctions arise because you have 5 cutting sequences (substituting for N in the second general pattern), and all ligations are possible: 5x5=25. To these you would have to add the possible junctions of the other cutters, C^TNAG and T^TAA, which give you and additional 5 cutting patterns for a total of 10 cutting sequence. This means, if I am correct, that you have 10x10=100 possible junctions. You have some work to do here, but the syntax is as indicated (each possible ligation separated by a | symbol):

You can name this 100-sequence ligation pattern "myCocktail" or whatever you want, and then address it as such when you run juicer.sh, with the -s switch

myCocktail) ligation="'(xxxx|xxxx|your 100 ligation junctions...)'"

notice the double quote followed (or preceded) by a single quote at the start (or end)

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