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
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
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
