metaloci 1.0.1

METALoci: spatially auto-correlated signals in 3D genomes

METALoci

Spatially auto-correlated signals in 3D genomes.

METALoci relies on spatial autocorrelation analysis, classically employed in geostatistics, to describe how the variation of a variable depends on space at a global and local scales (e.g., identifying contamination hotspots within a city). METALoci repurposes this type of analysis to quantify spatial genome hubs of similar epigenetic properties. Briefly, the overall flowchart of METALoci consists of four steps:

• First, a genome-wide Hi-C normalized matrix is taken as input and the top interactions selected.

• Second, the selected interactions are used to build a graph layout (equivalent to a physical map) using the Kamada-Kawai algorithm with nodes representing bins in the Hi-C matrix and the 2D distance between the nodes being inversely proportional to their normalized Hi-C interaction frequency.

• Third, epigenetic/genomic signals, measured as coverage per genomic bin (e.g., ChIP-Seq signal for H3K27ac), are next mapped into the nodes of the graph layout.

• The fourth and final step involves the use of a measure of autocorrelation (specifically, the Local Moran’s I or LMI) to identify nodes and their neighborhoods with an enrichment of similar epigenetic/genomic signals.

METALoci is compatible with .cool, .mcool and .hic Hi-C formats; and with .bed signal files. The signal used in METALoci may be any numerical signal (as long as it is in a .bed file, with the location of such signal).

Have a look at the documentation!

Installation

METALoci requires bedtools to be installed and accesible from the conda environment you will use. You can install it with

conda install bedtools

Install metaloci from PyPI:

conda create -n metaloci python==3.9
conda activate metaloci
pip install metaloci

If you are experiencing any unexpected results with METALoci, we suggest to update the version of awk you are using. The recommended version is 1.3.4 or newer.

In Ubuntu, you can do this with:

sudo apt install mawk

Contributors

METALoci is currently being developed at the MarciusLab by Iago Maceda, Marc A. Marti-Renom and Leo Zuber, with the contribution of other members of the lab.