Unequal number of contacts after hicNormalize --normalize smallest

[Ma-Mes]

Hi developers,

thanks for your very useful tool.
I have two .mcool matrices with several resolutions which I want to compare. hicCorrectMatrix diagnostic_plot tells me, that at 1MB resolution, matrix A has around 27,000 counts per bin and matrix B has around 10,000. At 100 kb resolution, matrix A has around 2,700 counts and matrix B has around 1,000. That fits very well.
As I want to compare them, I normalize them together with hicNormalize --normalize smallest. For the 1 MB resolution, all is fine (around 10,000 counts for both matrices). But I get a weird output for the 100 kb resolution: matrix A has only around 100 counts while matrix B has the expected 1,000 counts. I checked my code to be sure not mixing up resolutions.
Could that result from using .mcool files? Thanks for your suggestions.

Best,
Maxim

[Ma-Mes]

You can also see it with hicInfo.

That's the output for the 1MB resolution after normalization:

Matrix information file. Created with HiCExplorer's hicInfo version 3.7.6

File: matrixB.smallest.1000000.mcool
Date: 2025-11-25T09:27:44.526907
Genome assembly: unknown
Size: 4,025
Bin_length: 1000000
Chromosomes:length: chr_1: 501967303 bp; chr_2: 650458083 bp; chr_3: 627456150 bp; chr_4: 525206139 bp; chr_5: 576238907 bp; chr_6: 495363004 bp; chr_7: 644841383 bp;
Number of chromosomes: 7
Non-zero elements: 7,099,084
The following columns are available: ['chrom' 'start' 'end']
Generated by: HiCMatrix-17.2
Cooler library version: cooler-0.10.4
HiCMatrix url: https://github.com/deeptools/HiCMatrix

Matrix information file. Created with HiCExplorer's hicInfo version 3.7.6

File: matrixA.smallest.1000000.mcool
Date: 2025-11-25T09:27:46.301642
Genome assembly: unknown
Size: 4,025
Bin_length: 1000000
Chromosomes:length: chr_1: 501967303 bp; chr_2: 650458083 bp; chr_3: 627456150 bp; chr_4: 525206139 bp; chr_5: 576238907 bp; chr_6: 495363004 bp; chr_7: 644841383 bp;
Number of chromosomes: 7
Non-zero elements: 7,834,244
The following columns are available: ['chrom' 'start' 'end']
Generated by: HiCMatrix-17.2
Cooler library version: cooler-0.10.4
HiCMatrix url: https://github.com/deeptools/HiCMatrix

And here for the 100kb resolution after normalization:

Matrix information file. Created with HiCExplorer's hicInfo version 3.7.6

File: matrixB.smallest.100000.mcool
Date: 2025-11-25T09:27:39.327960
Genome assembly: unknown
Size: 40,219
Bin_length: 100000
Chromosomes:length: chr_1: 501967303 bp; chr_2: 650458083 bp; chr_3: 627456150 bp; chr_4: 525206139 bp; chr_5: 576238907 bp; chr_6: 495363004 bp; chr_7: 644841383 bp;
Number of chromosomes: 7
Non-zero elements: 22,644,533
The following columns are available: ['chrom' 'start' 'end']
Generated by: HiCMatrix-17.2
Cooler library version: cooler-0.10.4
HiCMatrix url: https://github.com/deeptools/HiCMatrix

Matrix information file. Created with HiCExplorer's hicInfo version 3.7.6

File: matrixA.smallest.100000.mcool
Date: 2025-11-25T09:27:40.667580
Genome assembly: unknown
Size: 40,219
Bin_length: 100000
Chromosomes:length: chr_1: 501967303 bp; chr_2: 650458083 bp; chr_3: 627456150 bp; chr_4: 525206139 bp; chr_5: 576238907 bp; chr_6: 495363004 bp; chr_7: 644841383 bp;
Number of chromosomes: 7
Non-zero elements: 1,322,422
The following columns are available: ['chrom' 'start' 'end']
Generated by: HiCMatrix-17.2
Cooler library version: cooler-0.10.4
HiCMatrix url: https://github.com/deeptools/HiCMatrix