d5932e4051a4885f0036831cdfc5fbf1eb08a499 lrnassar Tue Oct 10 17:16:27 2023 -0700 Fixing broken blog links, refs #32439 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index e97207e..7f35b02 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -105,31 +105,31 @@ The first three required BED fields are: </p> <ol> <li> <strong>chrom</strong> - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).</li> <li> <strong>chromStart</strong> - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.</li> <li> <strong>chromEnd</strong> - The ending position of the feature in the chromosome or scaffold. The <em>chromEnd</em> base is not included in the display of the feature, however, the number in <a href="FAQtracks#tracks1">position format</a> will be represented. For example, the first 100 bases of chromosome 1 are defined as <em>chrom=1, chromStart=0, chromEnd=100</em>, and span the bases numbered 0-99 in our software (not 0-100), but will represent the position notation chr1:1-100. Read more - <a href="http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/">here</a>. + <a href="https://genome-blog.gi.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/">here</a>. <br><em>chromStart</em> and <em>chromEnd</em> can be identical, creating a feature of length 0, commonly used for insertions. For example, use <em>chromStart=0, chromEnd=0</em> to represent an insertion before the first nucleotide of a chromosome.</li> </ol> <p>The 9 additional optional BED fields are:</p> <ol start=4> <li> <strong>name</strong> - 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.</li> <li> <strong>score</strong> - A score between 0 and 1000. If the track line <em>useScore</em> attribute is set to 1 for this annotation data set, the <em>score</em> 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: