HiC maps differ when two files loaded [BUG]

[batzza]

Describe the bug I am attempting to compare two .hic files -- one from 4DN portal and one locally generated. The files differ when loaded together and the output depends on which is loaded as A or B map.

To Reproduce If you are interested in following up, I may be able to share the hic file but I need to check with my PI before sharing this unpublished data.

Expected behavior The mapping of the file should not be altered when both are loaded.

Screenshots If I load the files individually, they look very similar but when loaded together they are radically different.

4DN file:

local file:

However, when they are both loaded, the maps are altered.

If I load the 4DN file then add my local as "B" map:The 4DN file is unchanged:

but the local file is changed:

Conversely, if I load the local file first than add the 4DN file as the "B" map, the local map is unchanged:

but the 4DN file is altered:

This behavior is identical in the latest desktop version.

Desktop (please complete the following information):

• OS: macOS Mojave
• Version 1.11.08

Additional context Local file is unpublished, I would need to discuss with my PI to share.

[batzza]

Additionally, these maps do not differ when viewed simultaneously in WashU Epigenome Browser:

[sa501428]

For Juicebox Web issues, please post to https://github.com/igvteam/juicebox.js (managed by @jrobinso et al.) You could try viewing the maps in Juicebox Desktop as well.

[batzza]

As I stated, the issue is exactly the same in the desktop version.

Local D60 file loaded alone on desktop version:

4DN file loaded alone on desktop version:

4DN file loaded with D60 file added as control on desktop version (showing observed vs control):

Local D60 file loaded with 4DN file loaded as control on desktop version (showing observed vs control):

[sa501428]

Ah apologies, I missed that last part. What happens when you run java -jar juicer_tools.jar validate <hicfile> on both of the files? (using the latest jar under https://github.com/aidenlab/Juicebox/releases)

[batzza]

No worries.

D60 validation output:

$ juicer_tools validate ../data/020_final_output/hic/D060.hic
Reading file: ../data/020_final_output/hic/D060.hic
File has normalization: VC
Description: Coverage
File has normalization: VC_SQRT
Description: Coverage (Sqrt)
File has normalization: KR
Description: Balanced
File has zoom: BP_2500000
File has zoom: BP_1000000
File has zoom: BP_500000
File has zoom: BP_250000
File has zoom: BP_100000
File has zoom: BP_50000
File has zoom: BP_25000
File has zoom: BP_10000
File has zoom: BP_5000
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(-: Validation successful

and for 4DN file:

$ juicer_tools validate ../data/999_external/4DNFII6AN691.hic
Reading file: ../data/999_external/4DNFII6AN691.hic
File has normalization: VC
Description: Coverage
File has normalization: VC_SQRT
Description: Coverage (Sqrt)
File has normalization: KR
Description: Balanced
File has zoom: BP_10000000
File has zoom: BP_5000000
File has zoom: BP_2500000
File has zoom: BP_1000000
File has zoom: BP_500000
File has zoom: BP_250000
File has zoom: BP_100000
File has zoom: BP_50000
File has zoom: BP_25000
File has zoom: BP_10000
File has zoom: BP_5000
File has zoom: BP_2000
File has zoom: BP_1000
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(-: Validation successful

Both appear valid but maybe the issue stems from the different number of resolutions in the two files?

EDIT Apologies, missed the link to use the latest jar. The above output was generated with Juicer Tools v1.22.01. However, I re-ran the command with the latest jar (v2.13.07) and got identical validation results.