Interval format
From BioUML platform
Revision as of 16:40, 17 May 2013 by BioUML wiki Bot (Talk | contribs)
- File format title
- Interval format (*.interval)
- Element type
track
- Plugin
- ru.biosoft.bsa (Bio-sequences analyses plugin)
Description
The interval format is pretty much like BED format, but only first three columns are well-defined; others can be used for any purpose.
The first three required fields are:
- chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
- chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
- chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
Other fields (if exist) will be loaded into site properties with names field1, field2 and so on.
Example
Here's an example of track in interval format with additional allele information:
chr22 1000 1001 A C chr22 1005 1005 - GT chr22 1010 1012 GC T
