Trouble processing new ENCODE Hi-C files using juicer_tools

[Kristy Mualim]

Hello! 

Thank you so much for processing and uploading the latest hg38 Hi-C files onto ENCODE. 

I have a couple of questions regarding this. 

I've been trying to process the latest hg38 Hi-C files that were uploaded onto ENCODE: https://www.encodeproject.org/experiments/ENCSR477GZK/ (as an example) 

and am having trouble using juicer_tools to extract the data from the Hi-C files. 

Version of juicer_tools: juicer_tools_1.13.02.jar

Command: java -jar juicer_tools_1.13.02.jar dump observed NONE ENCFF573OPJ.hic  1 1 BP 5000 chr1/chr1.observed

Traceback: 

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

WARN [2022-03-14T11:50:10,708]  [Globals.java:138] [main]  Development mode is enabled

Error reading datasetnull

Could not read hic file: null

I've double-checked the hic file to ensure it's not actually null, having re-downloaded it from the ENCODE portal multiple times just to be sure. Using `hic-straw`, I can confirm that the hic file is not null. Would you have any tips on making this work? 

In addition, what would be the best way to extract the normalization available in the hic file? I've tried looking into this colab: https://colab.research.google.com/drive/1548GgZe7ndeZseaIQ1YQxnB5rMZWSsSj but that command wasn't available. 

Best, 

Kristy

[Moshe Olshansky]

Hi Kristy,

It is possible that the hic file is version 9 and  juicer_tools_1.13.02.jar can not read this new version. Try a newer version of juicer_tools (say 1.22.01 or may be even 2.13.07).

Best regards,

Moshe.