SELFISH

SELFISH (Discovery of Differential Chromatin Interactions via a Self-Similarity Measure) is a tool by Abbas Roayaei Ardakany, Ferhat Ay, and Stefano Lonardi. It is currently maintained by Tuvan Gezer ([email protected]). SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps. It uses self-similarity to model interactions in a robust way. For more information read the full paper: Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure.

Installation and usage

PIP

pip3 install selfish-hic
selfish -f1 /path/to/contact/map1.txt \
        -f2 /path/to/contact/map2.txt \
	-ch 2 \
        -r 100kb -o ./output.npy

Github

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

git clone https://github.com/ay-lab/selfish
./selfish/selfish/selfish.py -f1 /path/to/contact/map1.txt \
                             -f2 /path/to/contact/map2.txt \
	                     -ch 2 \
                             -r 100kb -o ./output.npy

Nextflow

If you have any problem regarding dependencies or version mismatches, we recommend using Nextflow with a container technology like Docker or Singularity. These methods require Nextflow(Can be installed with a single command that doesn't require special permissions.), and the desired container technology to be available. Program arguments are given to Nextflow with two dashes and the short format listed below. Updating: If Nextflow warns that your project is outdated, use nextflow pull ay-lab/selfish in order to update to latest version.

Install Nextflow

Nextflow works for Linux and OS X. Install it using one of the commands listed below. Requires Java 8+

wget -qO- https://get.nextflow.io | bash
OR
curl -s https://get.nextflow.io | bash

With Docker

./nextflow run ay-lab/selfish --f1="/path/to/contact/map1.txt" \
                              --f2="/path/to/contact/map2.txt" \
	                      --ch=2 \
                              --r=100kb -profile docker

With Singularity

./nextflow run ay-lab/selfish --f1="/.../map1.txt" \
                              --f2="/.../map2.txt" \
	                      --ch=2 \
                              --r=100kb -profile singularity

Bioconda

Bioconda install isn't currently available.

Dependencies

Selfish uses some python packages to accomplish its mission. These are the packages used by selfish:

numpy
pandas
matplotlib
seaborn
scipy
statsmodels
hic-straw
pathlib

Parameters

Short	Long	Meaning
Required Parameters
-f1	--file1	Location of contact map 1. (See below for format.) Not required for HiC-Pro input.
-f2	--file2	Location of contact map 2. (See below for format.) Not required for HiC-Pro input.
-r	--resolution	Resolution of the provided contact maps.
-o	--outfile	Name of the output file.
-ch	--chromosome	Specify which chromosome to run the program for.
-m1	--matrix1	Location of matrix file, only for HiC-Pro type input.
-m2	--matrix2	Location of matrix file, only for HiC-Pro type input.
-bed1	--bed1	Location of bed file, only for HiC-Pro type input.
-bed2	--bed2	Location of bed file, only for HiC-Pro type input.
Optional Parameters
-b1	--biases1	Location of biases file for contact map 1. (See below for format.)
-b2	--biases2	Location of biases file for contact map 2. (See below for format.)
-sz	--sigmaZero	Sigma0 parameter for Selfish. Default is experimentally chosen for 5Kb resolution.
-i	--iterations	Iteration count parameter for Selfish. Default is experimentally chosen for 5Kb resolution.
-v	--verbose	Whether the program prints its progress while running. Default is True.
-p	--plot	Whether the program plots its results. Highly discouraged for high resolutions(<50kb) as it will take a lot of time to compute the plots. For high resolutions, we recommend using the output matrix and plotting small sections of it manually. Default is False.
-lm	--lowmem	Use float32 instead of float64. Uses less memory at the cost of precision. Default is False.
-V	--version	Shows the version of the tool.

Input Formats

SELFISH supports 3 different input formats. Plain text, .hic, .cool, .bed/.matrix pairs (HiC-Pro format).

Text Contact Maps

Contact maps need to have the following format. They must not have a header. Values must be separated by either a space, a tab, or a comma.

Chromosome	Midpoint 1	Chromosome	Midpoint 2	Contact Count
chr1	5000	chr1	65000	438
chr1	5000	chr1	85000	12
...	...	...	...	...

Bed-Matrix pairs (HiC-Pro format)

User must provide a chromosome with the -ch argument. .bed and .matrix files must have the same name other than the extension. Either file name can be provided as an input for selfish and the program will search for the second file automatically.

HiC file

User must provide a chromosome with the -ch argument. Selfish uses juicer's straw tool to read .hic files.

.cool file

User must provide a chromosome with the -ch argument. Selfish uses cooler to read .cool files.

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.

Chromosome	Midpoint	Bias
chr1	5000	1.012
1	65000	1.158
...	...	...

Output

Output of Selfish is a matrix of p-values indicating the probability of differential conformation (Smaller values mean more significant.). X and Y coordinates indicate the bin midpoints. File format of the output is a binary numpy file. It can be read by using Numpy as follows.

import numpy as np
matrix = np.load("/path/to/output/selfish.npy")

phlya / selfish Goto Github PK

selfish's Introduction