iSeg: Genomic Segmentation


    Welcome to the iSeg genomic segementation portal, In this platform, you can obtain segmentation of any genetic profile with three steps. Please use the dialog below to complete a segmentation request. You will need a data file as a 4-column TSV (tab separated values) without headers. The first column should correspond to the chromosome name, the second and third columns must correspond to the start and end locations of the chromosome. The fourth column should correspond to gene expression (signal) values.

A should look like the below. You can also download a sample data file once you successfully log in. By default, the user has access to a guest account (data will be public). You can simply click the login button. Please do not hit the enter button to log in using the login dialog, click instead.
chr1     0     100     -0.14408
chr1     100     200     -0.36571
chr1     200     300     0.29442
chr1     300     400     -0.04224
chr1     400     500     -0.07938
chr1     500     600     0.13847
chr1     600     700     0.01411
chr1     700     800     -0.03773
chr1     800     900     -0.06862
chr1     900     1000     -0.09028





Step 1: Select Data Input

Enter the data as a file. A tab-limited TSV file, without quotes is the required format. The program is capable of reading in any C++ accessible input file. The following requirements must be satisfied for successful execution of the program.

  • The file must contain four columns.
  • The first column is the chromosome identifier. This is a string data type.
  • The second and third columns correspond to the start and end locations of the chromosome. These are numeric data types (integer or double).
  • The intensity of the signal (profile) must be in the fourth column. This is a numeric data type (double).
  • Here is a sample data file you can download for trial runs.

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    Enter the data file (Click button below)

    Upload file here

    Step 2: Choose Parameters

    In this form, you can enter the parameters for the iSeg program. If you are unclear about the input fields, simply press "Tab" and the fields will be highlighted.

    • Enter power factor. The default value is 1.1.
    • Enter minimum segmentation window length. The default value is 1.
    • Enter maximum segmentation window length. The default value is 300.
    • Enter the desired false discovery rate (FDR). The default value is 0.05.
    • Enter the initial segmentation threshold. The default value is 0.0001.
    • Enter the biological cut-off. A biological cut-off of 0, 0.5, 1, 2, 3, 4 are possible values. The default value is 1. For multiple cut-off runs, specify cut-off with dashes. For example, 0-5-7 will run iSeg for cut-offs 0, 5, and 7.
    • Enter the global non-zero parameter (NZP) for the profile. This is OPTIONAL. If left blank, the server will use the default value of one.
    • Choose segmentation output file format. You can type bed (default) for BED format, or raw for raw text format. Default is bed.
    • Do you want to generate a summary file (in xlsx format)? A summary file will NOT be generated by default.