BenxiaHu / DLR_ICF

DLR_ICF

This tutorial will introduce how to run DLR_ICF to analyze DLR and ICF.

DLR_ICF can be used to analyze DLR and ICF based on normlazed Hi-C contact matrix.

DLR: distal-to-local ratio
ICF: inter-chromosomal fraction

calculate the DIR and ICF for individual Hi-C contact matrix

usage:

DLR_ICF_main [-h] [-b] -I INPUTPATH -f FILENAME -d DISTANCE -r RESOLUTION -O OUTPATH -c CHRSIZE -o OUTFILE

the format of input file is cool format.
the output file is bedgraph which can be visualized in IGV/UCSC or other genome browsers.

example:

1. used the iced normalized contact matrix to calculate DLR/ICF.
   DLR_ICF_main **-b** -I "the path of matrix" -f "test" -d 1000000 -r 10000 -o 1Mb_test_10kb -O "the path of output" -c hg38.chrom.sizes

2. used the balanced contact matrix (mcool) to calculate DLR/ICF.
   DLR_ICF_main -I "the path of matrix" -f "test" -d 1000000 -r 10000 -o 1Mb_test_10kb -O "the path of output" -c hg38.chrom.sizes

optional arguments:

-h		--help		show this help message and exit
-b		--balanced		contact matrix is iced or balanced
-I	INPUTPATH	--inputpath	INPUTPATH	path of input file
-f	FILENAME	--filename	FILENAME	name of input file
-d	DISTANCE	--distance	DISTANCE	the distance of distal chromation interactions
-r	RESOLUTION	--resolution	RESOLUTION	resolution of contact matrix
-O	OUTPATH	--outpath	OUTPATH	path of output file
-c	CHRSIZE	--chrsize	CHRSIZE	chromosome size file
-o	OUTFILE	--outfile	OUTFILE	name of output file

calculate gene-wise DIR and ICF for individual Hi-C contact matrix

usage:

DLR_ICF_gene [-h] [-b] -I INPUTPATH -f FILENAME -d DISTANCE -r RESOLUTION -g "hg38_gene.bed" -O OUTPATH -c CHRSIZE -o OUTFILE

the format of input file is cool format.
the output file is bedgraph which can be visualized in IGV/UCSC or other genome browsers.

example:

1. used the iced normalized contact matrix to calculate gene-wise DLR/ICF.
   DLR_ICF_gene **-b** -I "the path of matrix" -f "test" -d 1000000 -r 10000 -o 1Mb_test_10kb -g "hg38_gene.bed" -O "the path of output" -c hg38.chrom.sizes

2. used the balanced contact matrix (mcool) to calculate gene-wise DLR/ICF.
   DLR_ICF_gene -I "the path of matrix" -f "test" -d 1000000 -r 10000 -o 1Mb_test_10kb -g "hg38_gene.bed" -O "the path of output" -c hg38.chrom.sizes

optional arguments:

-h		--help		show this help message and exit
-b		--balanced		contact matrix is iced or balanced
-I	INPUTPATH	--inputpath	INPUTPATH	path of input file
-f	FILENAME	--filename	FILENAME	name of input file
-d	DISTANCE	--distance	DISTANCE	the distance of distal chromation interactions
-r	RESOLUTION	--resolution	RESOLUTION	resolution of contact matrix
-g	genebody	--genebody	genebody	genebody bed file
-O	OUTPATH	--outpath	OUTPATH	path of output file
-c	CHRSIZE	--chrsize	CHRSIZE	chromosome size file
-o	OUTFILE	--outfile	OUTFILE	name of output file

divide the DIR and ICF into different groups based on compartment definitions.

DLR_ICF_separation [-h] [-b] -I INPUTPATH -f FILENAME -d DISTANCE -p Compartment -r RESOLUTION -O OUTPATH -c CHRSIZE -o OUTFILE

optional arguments:

-h		--help		show this help message and exit
-b		--balanced		contact matrix is iced or balanced
-I	INPUTPATH	--inputpath	INPUTPATH	path of input file
-f	FILENAME	--filename	FILENAME	name of input file
-d	DISTANCE	--distance	DISTANCE	the distance of distal chromation interactions
-p	compartment	--compartment	compartment	compartment of chromaitn
-r	RESOLUTION	--resolution	RESOLUTION	resolution of contact matrix
-O	OUTPATH	--outpath	OUTPATH	path of output file
-c	CHRSIZE	--chrsize	CHRSIZE	chromosome size file
-o	OUTFILE	--outfile	OUTFILE	name of output file

output ICF groups.

ICF_chromatin [-h] [-b] -I INPUTPATH -f FILENAME -p Compartment -r RESOLUTION -O OUTPATH -c CHRSIZE -o OUTFILE

optional arguments:

-h		--help		show this help message and exit
-b		--balanced		contact matrix is iced or balanced
-I	INPUTPATH	--inputpath	INPUTPATH	path of input file
-f	FILENAME	--filename	FILENAME	name of input file
-p	compartment	--compartment	compartment	compartment of chromaitn
-r	RESOLUTION	--resolution	RESOLUTION	resolution of contact matrix
-O	OUTPATH	--outpath	OUTPATH	path of output file
-c	CHRSIZE	--chrsize	CHRSIZE	chromosome size file
-o	OUTFILE	--outfile	OUTFILE	name of output file

compare the difference in the DIR and ICF for 2 Hi-C contact matrices.

usage:

DLR_ICF_comparison [-h] -i INPUTPATH -t TREATMENT -c CONTROL -r RESOLUTION -O OUTPATH -o OUTFILE

example:
DLR_ICF_comparison -i "the path of matrix" t "caseid" -c "controlid" -r 10000 -o 1Mb_test_10kb -O "the path of output"

Here we convert the DLR/ICF ratio into z-score, and calculate p value and fdr.

the output file is bedgraph which can be visualized in IGV/UCSC or other genome browsers.

optional arguments:

-h		--help		show this help message and exit
-i	INPUTPATH	--inputpath	INPUTPATH	path of input file
-t	TREATMENT	--treatment	TREATMENT	name of treatment file
-c	CONTROL	--control	CONTROL	name of control file
-r	RESOLUTION	--resolution	RESOLUTION	resolution of contact matrix
-O	OUTPATH	--outpath	OUTPATH	path of output file
-o	OUTFILE	--outfile	OUTFILE	name of output file

Installation

requirement for installation

python>=3.8
numpy
pandas
argparse
cooler
h5py
scipy.stats
statsmodels.stats.multitest
bioframe

pip install DLR-ICF==1.0.7

https://pypi.org/project/DLR-ICF/1.0.7/

conda install -c bxhu dlr_icf

https://anaconda.org/bxhu/dlr_icf

Reference

Transcription Elongation Can Affect Genome 3D Structure (https://doi.org/10.1016/j.cell.2018.07.047)