2D Functions
A. Purpose
To create a binary hic format file containing contact matrices at different resolutions and normalized by different methods from a text file describing mapped Hi-C reads
B.Test Data
An example test data is the GM06990 cell line data, that can be downloaded from link below:
- GM06990 Cell line:
- Bowtie2: http://sysbio.rnet.missouri.edu/bdm_download/GenomeFlow/GM06990/GenomeFlow_formatted.bowtie2.input
- Bwa: http://sysbio.rnet.missouri.edu/bdm_download/GenomeFlow/GM06990/GenomeFlow_formatted.bwa.input
C. Output
A binary .hic file containing contact matrices
D. Running
Access the function from the menu toolbar: 2D-Functions/Convert to HiC
E. Convert mapped Hi-C reads to .hic file GUI
| Field | Description | Default |
|---|---|---|
| Input file | A text file describes mapped Hi-C reads (format described above) | NA |
| Genome ID | Version genome of Hi-C data | hg19 |
| Output File | A name of the output hic format file | NA |
| Contact Threshold | Number of interaction threshold for contacts to be used in creating contact matrices. | 0 |
| MAPQ Score Threshold | Mapping quality score threshold for reads to be considered in creating contact matrices. | 0 |
| Chromosomes | Chromosomes for which their contact matrices need to be created. When left blank, all chromosomes will be considered. Chromosomes must be separated by a comma (,). | All (when left blank) |
| Resolutions | List of resolutions of contact matrices to be created. Resolutions are separated by a comma (,) | 2500000, 1000000, 500000, 250000, 100000, 50000, 25000,10000,5000 |
| Restriction Site File | Each line starts with a chromosome number followed by positions of restriction sites on that chromosome, in numeric order, and ending with the size of the chromosome. When provided, 8 additional fragment-delimited resolutions are added: 500f, 250f, 100f, 50f, 20f, 5f, 2f, 1f | blank |
A. Purpose
To extract a contact matrix from a hic file into a sparse matrix format in a text file.
B. Input
A local path to a hic file or an online link to a hic file. A link to a hic file: https://www.encodeproject.org/files/ENCFF219YOB/@@download/ENCFF219YOB.hic
C. Output
A contact matrix in sparse matrix format
D. Running
Access the function from the menu toolbar: 2D-Functions/Extract HiC
E. Extract contact matrices from a hic file GUI
| Field | Description | Default |
|---|---|---|
| Path to .hic File | An online link or local path to a hic format file | NA |
| Load | Click this button to fetch information from the header of the hic file. | NA |
| Genome | Genome version of the hic file | NA |
| Chromosomes | List of resolutions of contact matrices in the hic file | NA |
| From | Start of a fragment (to extract its contact matrix). When From and To are left blank, the whole chromosome is considered. | Blank |
| To | End of a fragment (to extract its contact matrix). When From and To are left blank, the whole chromosome is considered. | Blank |
| Resolution | List of resolutions of contact matrices in the hic file | NA |
| Normalization | List of normalization methods used to normalize contact matrices | NA |
| Extract Contac Data | Click this button to initiate extracting contact data | NA |
A. Purpose
To normalize a un-normalized contact matrices in sparse matrix format.
B. Input
A contact matrix in sparse matrix format.
C. Output
A normalized contact matrix in sparse matrix format. The matrix is normalized by the Iterative Correction and Eigenvector decomposition (ICE) method
D. Running\
Access the function from the menu toolbar: 2D-Functions/Normalized HiC Data
E. Normalize an unnormalized HiC contact matrices GUI
A. Purpose
To create a two dimensional (2D) graphical representation of a contact matrix from an input file.
B. Input
A sparse matrix format or a square matrix format. Mark the Is Square Matrix? box if the input is a square matrix.
- An example sparse matrix file can be found here:
/executable/sample_data/ contact_matrices/ chr11_10kb_gm12878_list_125mb_135mb.txt - Examples of square matrix files can be found here:
/executable/sample_data/ contact_matrices/square_matrices/
Note: Resolution for square matrices = 40000
C. Output
A Heatmap which is a graphical representation of contact data where numeric values in the input contact matrix are represented as colors based according to a selected color gradient.
D. Running
Access the function from the menu toolbar: 2D-Functions/Visualize Dataset.
E. Visualization GUI
| Field | Description | Default |
|---|---|---|
| Draw Title | It shows or hides the Heatmap title | checked |
| Draw Legend | It shows or hides the color legend | checked |
| Draw X-Axis Title | It shows or hides the X-axis title label on the 2D display window | checked |
| Draw X-Axis Ticks | It shows or hides the X-axis ticks label on the 2D display window | checked |
| Draw Y-Axis Title | It shows or hides the Y-axis title label on the 2D display window | checked |
| Draw Y-Axis Ticks | It shows or hides the Y-axis ticks label on the 2D display window | checked |
| Heatmap Direction(Left/Right) | It changes the Y-axis origin of the heatmap matrix from the Bottom-Left to Top-Left and vice versa | checked |
| Enable Zoom Mode | It allows the user to zoom in/out of the heat map matrix | unchecked |
| Is Square Matrix?(Input contact file) | Allows the user to specify if the input is a Square matrix (a full matrix) or a sparse matrix. If checked, it displays a textbox for the user to specify the matrix resolution. | unchecked |
| Specify Resolution | It is visible only if Is SquareMatrix? is checked. It allows user specify resolution for the input matrix. | NA |
| Input contact file | A text file containing a contact matrix in any of the format described above. | NA |
| Title | Allows user to specify the title of the heatmap | Heatmap Display |
| X-Axis Title | Allows user to specify the X-Axis title for the heatmap | Genome bin Resolution (bp) |
| Y-Axis Title | Allows user to specify the Y-Axis title for the heatmap | Genome bin Resolution (bp) |
| X min | It allows the user to specify the minimum X-axis Tick for the heatmap | 0 |
| X max | It allows the user to specify the maximum X-axis Tick for the heatmap | 200 |
| Y min | It allows the user to specify the minimum Y-axis Tick for the heatmap | 0 |
| Y max | It allows the user to specify the maximum Y-axis Tick for the heatmap | 200 |
| X min [Genome Location Equivalent] | It shows the genomic position equivalent for the minimum X-axis Tick for the heatmap | 0 |
| X max[Genome Location Equivalent] | It shows the genomic position equivalent for the maximum X-axis Tick for the heatmap | 8000000 |
| Y min [Genome Location Equivalent] | It shows the genomic position equivalent for the minimum Y-axis Tick for the heatmap | 0 |
| Y [Genome Location Equivalent] | It shows the genomic position equivalent for the maximum Y-axis Tick for the heatmap | 8000000 |
| Number of Units detected | It shows the number of regions found in the input matrix | 200 |
| Number of Missing Units | It shows the number of gaps or missing regions noted from the input matrix | 0 |
| Resolution detected | It displays the resolution of the input matrix | 40000 |
| Initial Start Position | It shows the minimum genome position observed from the input matrix | 0 |
| Initial End Position | It shows the maximum genome position observed from the input matrix | 8000000 |
| Gradient | An array of Color used as a gradient. One color is used as the bottom gradient and another color is used as the top gradient. Hence, it produces a gradient from one color to the other. The Gradient Colors are explained below | HOT |
| GRADIENT_BLACK_TO_WHITE | Produces a gradient from black (low) to white (high) | |
| GRADIENT_BLUE_TO_RED | Produces a gradient from blue (low) to red (high) | |
| GRADIENT_HEAT | Produces a different gradient for hot things (black, brown, orange, white) | |
| GRADIENT_HOT | Produces a gradient for hot things (black, red, orange, yellow, white) | |
| GRADIENT_MAROON_TO_GOLD | Produces a gradient from maroon (low) to gold (high) | |
| GRADIENT_RAINBOW | Produces a gradient through the rainbow: violet, blue, green, yellow, orange, red | |
| GRADIENT_RED_TO_GREEN | Produces a gradient from red (low) to green (high) | |
| GRADIENT_ROY | Produces a gradient through red, orange, yellow | |
| Data Type | It determines the type of data to be displayed. The types available are the raw input data, a Tanh of input data, a Pearson correlation of input data, and a Spearman correlation of the input data. | TANH |
A .Purpose
To identify Topological Associated domains(TAD) from input contact matrix.
B. Input
An input file in square matrix format or a sparse matrix format .
An example sparse matrix file can be found here:
/executable/sample_data/ contact_matrices/ chr11_10kb_gm12878_list_125mb_135mb.txt
C. Output
A TAD with the best quality will be generated prefixed with BestTAD_ in bed format. This file will be found here: /Selected_output_directory_from_GUI/Output/TADs/.
D. Running
Access the function from the menu toolbar: 2D-Functions/Identify TAD.
E. Identify TAD GUI
| Field | Description | Default |
|---|---|---|
| Input contact file | An input file in any of the format described above | NA |
| Output folder | Directory to output the comparison report | NA |
| Is SquareMatrix?(Input contact file) | Allows the user to specify if the input is a Square matrix (a full matrix) or a sparse matrix. If checked, it displays a textbox for the user to specify the matrix resolution. | unchecked |
| Data Resolution | It is visible only if Is SquareMatrix? is checked. It allows user specify resolution for the input matrix. | 40000 |
| Chromosome (optional) | Allows user to specify the chromosome data | X |
| Run ClusterTAD Algorithm | The default algorithm used for TAD identification from the input contact Matrix checked | |
| Run | To start the identification process. A progress bar is displayed to show the steps taken by the TAD identification algorithm,. | NA |
| Stop | During the identification, if this button is pressed, the program will stop. | NA |
A. Purpose
To compare two TADs from two different Topological Associated domains(TAD) identification method.
B. Input
A file containing TADs in .bed format. The method whose TADs consistency is to be checked is termed Method-1, and the methods whose TADs is to be compared with is termed Method-2. Choose the same chromosome for different methods.
For example, to compare TAD from ClusterTAD with DI for chromosome 17,
Method-1 = /executable/sample_data/TAD_annotation/mESC_TAD_bed/ ClusterTAD /chr17.bed.
Method-2 = /executable/sample_data/TAD_annotation/mESC_TAD_bed/ DI /chr17.bed.
C. Output
A report of the consistency of the Method-1 with Method-2. The output reports the following cases:
Case 1 = The number of Exact TADs found in both Method-1 and Method-2
Case 2 = The number of Sub-TADs that exist between Method-1 and Method-2
Case 3 = The number of Conflicting TADs.
Case 4 = The number of TADs in Method-1 but not found in Method-2
D. Running
Access the function from the menu toolbar: 2D-Functions/Check TAD Consistency.
E. Check TAD consistency GUI
