Add .hic file with normalization in UCSC browser

[Marco DI STEFANO]

To whom this may concern,

I am trying to upload my Hi-C data on UCSC browser and I have problems to show the normalized files.

Briefly, what I did is the following:

1 - I generated .hic files from .allValidPairs file using the following command:

java -Xmx100g -jar ${JUICERJAR} pre ${allValidPairsFile} ${hicFile} ${GSIZE} -r 1000,2000,3000,5000,10000,15000,20000 -j 16 -v

where JUICERJAR=juicer_tools_1.22.01.jar and GSIZE is the file with the chromosome sizes in mm10. 

I am pretty sure this steps worked and that the final .hic file contains KR normalization weigths because if I run the command:

java -jar ${JUICERJAR} dump norm KR ${hicFile} 18 BP 1000

I obtain a list of weights dumped in the terminal as expected.

2 - When I load the file in the UCSC browser, I can see the raw data at all the expected resolution. 

However, if I go to the menu of the file, I cannot find any normalized map in the drop-down menu "Score normalization:", not even "KR" which I know is contained in the file.

3 - Next, I saw that only .hic versions 6-8 are accepted in the USCS browser, but I didn't find any way to downgrade my .hic files or to generate from the $allValidPairsFile a v8 .hic file.

Can you help me to solve this problem?

Thanks in advance for your work.

Best wishes,

Marco Di Stefano

Researcher

Chromatin and Cell Biology Group,

CNRS-Institute of Human Genetics,

Montpellier, France

Personal Web: es.linkedin.com/in/marcods

[Gerardo Perez]

Hello, Marco.

Thank you for your interest in the Genome Browser.

Could you share the URL to your HIC file? You can send it to our confidential support list at genom...@soe.ucsc.edu. We currently support HIC files up to version 9. We can check for the various components, such as the file version, byte-range access, etc.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on a publicly-accessible Google Groups forum.

Gerardo Perez
UCSC Genomics Institute

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