Mustache

Mustache(Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation) is a tool by Abbas Roayaei Ardakany, Ferhat Ay ([email protected]), Stefano Lonardi, and Halil Tuvan Gezer. Mustache is a tool for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps.Mustache uses recent technical advances in scale-space theory in Computer Vision to detect blob-shaped objects in a multi-scale representation of the contact map parametrized by the size of the smoothing kernel. For more information read the full paper: TBA.

Installation and usage

PIP

pip3 install mustache-hic
mustache -f /path/to/contact/map.txt \
         -r 100kb -o ./output.tsv

Github

Make sure you have Python 3 installed, along with all the dependencies listed.

git clone https://github.com/ay-lab/mustache
mustache -f /path/to/contact/map.txt \
         -r 100kb -o ./output.tsv

Dependencies

Mustach uses some python packages to accomplish its mission. These are the packages used by mustache:

1. numpy
2. pandas
3. matplotlib
4. seaborn
5. scipy
6. statsmodels
7. pathlib

Parameters

Short	Long	Meaning
Required Parameters
-f	--file	Location of contact map. (See below for format.)
-r	--resolution	Resolution of the provided contact map.
-o	--outfile	Name of the output file.
Optional Parameters
-b	--biases	Location of biases file for contact map. (See below for format.)
-sz	--sigmaZero	Sigma0 parameter for Mustache. Default is experimentally chosen for 5Kb resolution.
-oc	--octaves	Octaves parameter for Mustache. Default is 2.
-d	--distanceFilter	Distance filter parameter for Mustache. Loops are looked for within this distance. Default is 2Mb.
-i	--iterations	Iteration count parameter for Mustache. Default is experimentally chosen for 5Kb resolution.
-V	--version	Shows the version of the tool.

Input Formats

Text Contact Maps

Contact maps need to have the following format. They must not have a header. Values must be separated by a tab.

Midpoint 1	Midpoint 2	Contact Count
5000	65000	438
5000	85000	12
...	...	...

Bias File

Bias file need to have the following format. Bias file must use the same midpoint format as the contact maps. Bias file must not have a header. Bias file is a list of normalization factors. This means contacts will be divided by their corresponding factors.

Factor
NaN
1.12
0.1

Where the line number is equal to the bin number. So if your resolution is 5Kb, first line is the factor for 0-5Kb bin.

Output

Output of Mustache is a TSV file. It's format is as follows

| Bin 1 Chromosome | Bin 1 Start | Bin 1 End | Bin 2 Chromosome | Bin 2 Start | Bin 2 End | FDR | Mustache Scale for this Detection |