TADMaster Plus
The full TADMaster suite allows you to upload your chromosome contact data in a variety of input formats, select normalization methods to apply to your data, select methods to identify TADs, and visualize the results.
Complete the fields with the required information to get your job submission started: You can follow the example below
| Field | Description | Exmaple |
|---|---|---|
| Hi-C Format | Select the format that your input contact Hi-C data is in. We have provided 5 formats which are .hic, .cool, .h5, Square matrix (NxN), Sparse matrix (three-column) | Select SPARSE MATRIX |
| Title | Provide a title for your job submission | Example Job Submission Chr4 |
| Chromosome | Our tool can only extract TAD per chromosome. Hence specify the chromosome number for this job. Number only | 4 |
| Description | Provide a brief description of this Job. This will be helpful in case you make multiple submissions | Example Matrix dataset from 40-42.5Mb region of GM12878 dataset chromosome 4 |
| Provide the email address where we would send you a notification when your job is completed. Please confirm that the email address you provide is correct (optional) | "your email address" or leave blank | |
| Resolution | Resolution for the input contact matrix in basepairs. For example 40kb = 40000, 10kb = 10000 | 10000 |
Click on the Next Button to continue An example screenshot is provided below:
Select the Normalization Methods you want to be applied to the input data or Alternatively, you can skip normalization if your data is already normalized. For this example, we selected 2 normalization methods Vanilla Coverage (VC) and Iterative correction, and Eigenvector Decomposition (ICE) Click on the Next Button to continue
An example screenshot is provided below:
Select the TAD Methods to use for the TAD extraction out of the 12 provided. Select At least 2 methods Please note:
We selected to methods: Armatus and Topdom
- Review all the information and make sure they are correct.
- Upload your input dataset.
- Press the Back Button to Go back and make changes to your settings.
- The form will be automatically submitted once you submit the input data.
For this example, Upload the contact matrix in the format specified Download and Upload the Example Dataset provided Here
Finally, you get the submission report:
