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.
pip3 install mustache-hic
mustache -f /path/to/contact/map.txt \
-r 100kb -o ./output.tsv
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
Mustach uses some python packages to accomplish its mission. These are the packages used by mustache:
- numpy
- pandas
- matplotlib
- seaborn
- scipy
- statsmodels
- pathlib
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. |
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 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 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 |