What it does

This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type.

Note

The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output.

About formats

BED format Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:

The first three BED fields (required) are:

1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).

The additional BED fields (optional) are:

 4. name - The name of the BED line.
 5. score - A score between 0 and 1000.
 6. strand - Defines the strand - either '+' or '-'.
 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
 9. reserved - This should always be set to zero.
10. blockCount - The number of blocks (exons) in the BED line.
11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
13. expCount - The number of experiments.
14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.

Example

• For the following query:

  chr22  1000  4700  NM_174568 0 +
  

• running this tool with Window size as 1000, will return:

  chr22  1000  2000  NM_174568 0 +
  chr22  2000  3000  NM_174568 0 +
  chr22  3000  4000  NM_174568 0 +
  

• running this tool to make Sliding windows of size 1000 and offset 500, will return:

  chr22  1000  2000  NM_174568 0 +
  chr22  1500  2500  NM_174568 0 +
  chr22  2000  3000  NM_174568 0 +
  chr22  2500  3500  NM_174568 0 +
  chr22  3000  4000  NM_174568 0 +
  chr22  3500  4500  NM_174568 0 +