hicMergeMatrixBins (version 3.7.2+galaxy0)

**hicMergeMatrixBins** is used to decrease the resolution of a matrix. With this tool, you can for example create out of a 100 kb
contact matrix a 1000 kb one:

Number of bins to merge = 10

100 kb * 10 = 1000 kb = 1 Mb

Depending on the downstream analyses to perform on a Hi-C matrix generated with HiCExplorer, one might need different bin resolutions. For example using `hicPlotMatrix` to display chromatin interactions of a whole chromosome will not produce any meaningful vizualisation if it is performed on a matrix at restriction sites resolution (unmerged). Furthermore, the higher the resolution of a matrix, the more detailed it is, which can make it
difficult to interpret, especially if the read depth of the Hi-C data is not high enough. **hicMergeMatrixBins** address these issues by merging a given number of adjacent bins to reduce Hi-C matrices resolution.

To limit the loss of information, it is mandatory to perform **hicMergeMatrixBins** on matrices prior to any correction and any other bin merging (direct output from `hicBuildMatrix`). After bin merging, `hicCorrectMatrix` must be used for downstream analyses requiring corrected matrices.

**hicMergeMatrixBins** outputs a Hi-C matrix with reduced resolution.

Below, we will develop the example of a Hi-C matrix in *Drosophila melanogaster* that we want to display at the whole X-chromosome scale and at the scale of a 1Mb region of the X chromosome. To do this, we performed two different bin merging using **hicMergeMatrixBins** on an uncorrected matrix built at the restiction sites resolution using `hicBuildMatrix`.

Starting from a matrix with bins of a median length of 529bp (restriction enzyme resolution, here DpnII), running **hicMergeMatrixBins** with a number of bins to merge of 3 produced a matrix with bins of a median length of 1661bp, while **hicMergeMatrixBins** with a number of bins to merge of 50 produced a matrix with bins of a median length of 29798bp.

After the correction of these three matrices using `hicCorrectMatrix`, we plotted them using `hicPlotMatrix` at the scale of the whole X-chromosome and at the scale of the X:2000000-3000000 region to see the effect of bin merging on the interactions visualization.

**Effect of bins merging at the scale of a chromosome:**

When observed altogether, the plots above show that the merging of bins by 50 is the most adequate way to plot interactions for a whole chromosome in *Drosophila melanogaster* when starting from a matrix with bins of a median length of 529bp.

**Effect of bins merging at the scale of a specific region:**

When observed altogether, the plots above show that the merging of bins by 3 is the most adequate way to plot interactions for a region of 1Mb in Drosophila melanogaster when starting from a matrix with bins of a median length of 529bp.

For more information about HiCExplorer please consider our documentation on readthedocs.io