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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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More restriction enzyme sites of Arima than Juicer provided, how to modified juicer.sh #332

Open QianghuiZhu opened 9 months ago

QianghuiZhu commented 9 months ago

Hi! Juicer + 3D-DNA + juicebox is a great pipeline. I have run successfully for DpnII. But for Arima, I have some questions. I downloaded Hi-C data from VGP, and their Arima provided four restriction enzyme sites (GATC,GANTC,CTNAG,TTAA). But I found that _generate_sitepositions.py and juicer.sh only inculde two of these sites. image 1695715985832

So, My questions are: Q1: May I modify _generate_sitepositions.py line 56 to "'Arima' : [ 'GATC', 'GANTC', 'CTNAG', 'TTAA' ]," to contain all of four sites? Q2: If Q1 is yes, what should I modify in juicer.sh? Q3: Any other need to be modified or noticed?

Best!

AlcaArctica commented 6 months ago

I have the same question. Has there been any resolution?

QianghuiZhu commented 6 months ago

I have the same question. Has there been any resolution?

It seems that SALSA2 could provide four restriction enzyme sites.

sa501428 commented 6 months ago

Hi! Yes you can edit it and submit a pull request. (And of course, you can always edit downloaded code internally)

QianghuiZhu commented 6 months ago

Hi! Yes you can edit it and submit a pull request. (And of course, you can always edit downloaded code internally)

Thanks for this. But I do not know where should be edit. I do not clear that how to modified juicer.sh and other scripts. Best!