This tool is useful to compare two matrices in .h5 format by applying operations like difference, ratio or log2ratio after normalization. This can be used to determine the effect of a mutation compared to wild-type samples on contact enrichment, or to see TAD structure modifications near differentially expressed genes between two conditions when followed by hicPlotMatrix
. It can also be used to compare two biological replicates.
hicCompareMatrices
is usually perfomed on corrected matrices (hicCorrectMatrix
) with bins merged (hicMergeMatrixBins
) depending on the downstream analyses to perform. Here is an example of a log2ratio comparison between M1BP Knockdown and GST cells in Drosophila melanogaster on corrected matrices with 50 bins merged (about 30kb bins).
hicCompareMatrices -m \
M1BP_KD_merge_m50_corrected.h5 \
GST_merge_rf_m50_corrected.h5 \
--operation log2ratio -o m1bp_over_gst_log2_m50.h5
This code outputs a matrix containing the normalized log2ratio values of M1BP_KD_merge_m50_corrected.h5 over GST_merge_rf_m50_corrected.h5. We can then display this matrix using hicPlotMatrix
.
hicPlotMatrix -m \
m1bp_over_gst_log2_m50.h5 \
--clearMaskedBins \
--region chr2L:12,000,000-19,000,000 \
--vMin -4 --vMax 4 \
-o m1bp_over_gst_log2_m50_matrix_plot.png
In this plot we see that the cells with a M1BP Knockdown display a negative log2ratio compared to the wild-type. Depletion of M1BP thus show a dramatic effect on the distribution of Hi-C contacts in which short range contacts decrease (Ramirez et al. 2017, High-resolution TADs reveal DNA sequences underlying genome organization in flies, https://doi.org/10.1038/s41467-017-02525-w).
Below you can find an example of a log2ratio plot between Hi-C matrices of two biological replicates, no differences are observable which means that the replicates are well correlated.