juicer script on multiple restriction enzymes

[Chong Li]

To whom it may concern,

I am pretty new for juicer, and was recommended to use this to do the TAD calling and loop calling. My first challenge is how can I run the script for multiple restriction enzymes? I only see all the examples showed for only one enzyme and still cannot figure out how to apply for four enzymes: DpnII, DdeI, HinfI, and MseI.

Any incoming help would be appreciated so much!

[Neva Durand]

For the quickest and easiest solution, just run with restriction site "none".

Otherwise, you will need to make your own restriction site file using something along the lines of this script:

https://github.com/aidenlab/juicer/blob/master/misc/generate_site_positions.py

And then send in the ligation junction in a similar manner of what is done for Arima (see line 206 here: https://github.com/aidenlab/juicer/blob/master/CPU/juicer.sh)

You can send in the ligation junction with the -b flag and the restriction site file with the -y flag.

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[Corina Simian]

How exactly does that work? Do I need to run generate_site_positions.py for each enzyme and concatenate the resulting files? The script does not seem to support multiple enzymes at once.

Thanks!

[Muhammad Shamim]

The script does support multiple enzymes:

https://github.com/aidenlab/juicer/blob/encode/misc/generate_site_positions.py

See the example for Arima below. You can add in your own mix for multiple enzymes. 

There is a detailed description in the python file (lines 30-50) for pattern matching and wildcards.

patterns = {
    'HindIII'     : 'AAGCTT',
    'DpnII'       : 'GATC',
    'MboI'        : 'GATC',
    'Sau3AI'      : 'GATC',
    'Arima'       : [ 'GATC', 'GANTC' ],
  }

[Corina Simian]

Thanks a lot. That's very helpful.

[Norbert Bittner]

Hi Neva Durand,

do i need both the ligation junction setting (-b setting) (line 281 not 206 if i'm not mistaken) and the position site file (-y setting) or is the  -y setting enough?

Greets

Norbert

[Norbert Bittner]

Hi again.. And sorry to add to my previous question. I asked for both flags as in the Arima guide they only give the -y restriction site flag

https://arimagenomics.com/wp-content/files/Bioinformatics-User-Guide-Arima-HiC-and-Arima-High-Coverage-HiC.pdf

Page 10 / Bulletpoint 11

Thanks in advance

Norbert

Neva Durand schrieb am Freitag, 5. März 2021 um 20:12:55 UTC+1:

[Jun Kim]

Hi,

I have a related question. I'm also using Arima High Coverage kit. Is there an official website document stating the four restriction enzyme it uses is  DpnII, DdeI, HinfI, and MseI?

I emailed Arima but I haven't gotten a reply.
Thank you,

Jun

[Norbert Bittner]

Hi,

from Arima support i got the following restriction sites.

The 4 restriction enzymes included in the High Coverage HiC kit cut at the following recognition sites:

^GATC

G^ANTC

C^TNAG

T^TAA

^ is the cut site on the positive strand, 'N' can be any of the 4 genomic bases.

Greets

Norbert

[Ace]

Hi there,

A quick question regarding the multiple enzymes, if my data use a cocktail of enzymes that include HindIII, DpnII, and MboI, should I just add a new line after "Arima' and write it as a similar format so these lines become :

   patterns = {
    'HindIII'     : 'AAGCTT',
    'DpnII'       : 'GATC',
    'MboI'        : 'GATC',
    'Sau3AI'      : 'GATC',
    'Arima'       : [ 'GATC', 'GANTC' ],

    'example'       : [ 'AAGCTT', 'GATC' ,GATC],

  }

Thanks!

On Monday, January 17, 2022 at 11:27:17 PM UTC-5 sa50...@gmail.com wrote: