a3d3c1d713678d6306a96be69a1df93a82e0dfdd max Thu May 20 01:48:01 2021 -0700 adding chromStart=chromEnd case to BED docs, refs #24836 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index 5d50cd0..da83f65 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -100,31 +100,34 @@ The first three required BED fields are:

  1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
  2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
  3. chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature, however, the number in position format will be represented. For example, the first 100 bases of chromosome 1 are defined as chrom=1, chromStart=0, chromEnd=100, and span the bases numbered 0-99 in our software (not 0-100), but will represent the position notation chr1:1-100. Read more - here.
  4. + here. +
    chromStart and chromEnd can be identical, creating a feature of length 0, commonly + used for insertions. For example, use chromStart=0, chromEnd=0 to represent an insertion before the + first nucleotide of a chromosome.

The 9 additional optional BED fields are:

  1. name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
  2. score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray:
    shade