Argo File Formats: Simple Alignment

The simple alignment file format defined by the Broad is a tab-delimited file with 7 or more columns. Columns 1-7 define the alignment; the remaining columns are optional. You can use the optional columns for scores or other values to display and/or filter on.

The columns are:

  1. Alignment identifier
  2. Sequence 1 start coordinate
  3. Sequence 1 stop coordinate
  4. Sequence 2 start coordinate
  5. Sequence 2 stop coordinate
  6. Sequence 1 strand (1 or -1)
  7. Sequence 2 strand (1 or -1)

The default extension for simple alignment format files is .align. If you use this extension argo will automatically recognize your file as a simple alignment format file. Otherwise you will have to explicitly choose this format when prompted.

A sample alignment file can be found here.

Last Updated: Oct 22 2007
Contact: Reinhard Engels