Syntax

This tool converts a UCSC gene bed format file to a list of bed format lines corresponding to requested features of each gene.

• BED format Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and twelve 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 twelve 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.
  

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Example

• A UCSC gene bed format file:

  chr7 127475281 127491632 NM_000230 0 + 127486022 127488767 0 3 29,172,3225,    0,10713,13126
  chr7 127486011 127488900 D49487    0 + 127486022 127488767 0 2 155,490,        0,2399
  

• Converts the above file to a list of bed lines, which has the introns:

  chr7 127475311 127475993 NM_000230 0 +
  chr7 127486167 127488406 NM_000230 0 +
  chr7 127486167 127488409 D49487    0 +