This tutorial will introduce how to run DLR_ICF to analyze DLR and ICF.
DLR: distal-to-local ratio
ICF: inter-chromosomal fraction
DLR_ICF_main [-h] -F normal -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:
-
used the iced normalized contact matrix to calculate DLR/ICF.
DLR_ICF_main -F "ICE" -I "the path of matrix" -f "test" -d 1000000 -r 10000 -o 1Mb_test_10kb -O "the path of output" -c hg38.chrom.sizes -
used the balanced contact matrix (cool) to calculate DLR/ICF.
DLR_ICF_main -F "ICE" -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 | ||
| -F | format | --format | format of .cool file. | |
| -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 |
DLR_ICF_gene [-h] -F normal -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:
-
used the iced normalized contact matrix to calculate gene-wise DLR/ICF.
DLR_ICF_gene -f "ICE" -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 -
used the balanced contact matrix (cool) to calculate gene-wise DLR/ICF.
DLR_ICF_gene -f "ICE" -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 | ||
| -F | format | --format | format of .cool file. | |
| -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 |
DLR_ICF_separation [-h] -F normal -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 | ||
| -F | format | --format | format of .cool file. | |
| -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 |
ICF_chromatin [-h] -F "ICE" -I INPUTPATH -f FILENAME -p Compartment -r RESOLUTION -O OUTPATH -c CHRSIZE -o OUTFILE
optional arguments:
| -h | --help | show this help message and exit | ||
| -F | format | --format | format of .cool file. | |
| -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 |
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 |
python>=3.8
numpy
pandas
argparse
cooler
h5py
scipy.stats
statsmodels.stats.multitest
bioframe
https://pypi.org/project/DLR-ICF/1.10.0/
https://anaconda.org/bxhu/dlr_icf
- Transcription Elongation Can Affect Genome 3D Structure (https://doi.org/10.1016/j.cell.2018.07.047)
- Sickle cell disease induces chromatin introversion and ferroptosis in CD8+ T cells to suppress anti-tumor immunity (https://www.cell.com/immunity/fulltext/S1074-7613(25)00183-9)