Delta analyze allows users to upload own contact matrix to call TAD, interaction loop and predict 3D physical model. The results of pipeline can be directly loaded into Genome View, Topological View as well as Physical View. Delta uses TADtree to call TAD, FastHic to call interaction peak and BACH/MOGEN/HSA to predict 3D model. The whole procedure can be described as the following picture.

1.1 How to use pipeline?

1.1.1 Upload Matrix Data

Users need to upload an observed contact matrix M*M. Several rules need to be followed for matrix data:
1)The matrix data should only from one single chromosome
2)If the uploaded file has high resolution, we suggest compute an interested region instead of the whole chromosome.

An example of Interaction M*M Matrix data as follows:
11 197 175 154 140 147
197 11 210 138 124 98
175 210 33 348 143 110
154 138 348 44 176 171
140 124 143 176 55 448
147 98 110 171 448 66

1.1.2 General Parameters

Bin size: The bin size in the input contact matrix file
Scope
Chromosome: the chromosome number
Start Bin: the absolute bin index of start position, which can be computed by chromsome position/binsize.
End Bin: End Bin: the absolute bin index of end position, can be computed by chromosome position/binsize

1.1.3 Parameters for TAD

Delta uses TADtree to call TAD. The needed parameters are as follows:

1.1.4 Parameters for 3D model

Delta uses BACH or MOGEN to predict 3D physical model.

The required parameters and the default value for BACH are described as follows. Users need to set enzyme and reads length for the uploaded data to get an accurate model.

The required parameters and the default value for MOGEN are described as follows:

1.1.5 Email

Delta needs users to provide an email address to notify the complete of computing. When users click “Submit”, an email will be sent to the filled email address.

1.2 The Description of Results

1.2.1 Job Status

During the pipeline running procedure, the job status of each procedure will be updated live.

1.2.2 Calling TAD

When finished, the top 100 lines of TAD result will be shown.

1.2.3 Calling peak

When finished, the top 100 lines of Peak result will be shown.

1.2.4 3D model

When finished, the top 100 lines of result will be shown.