5df723f25a3b78158dac9e4c33d965e7b5878054 brianlee Wed Jul 13 07:46:36 2022 -0700 Highlighting step-by-step blog instructions inspired by MLQ refs #29747 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index 4d911e2..a11099c 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -86,31 +86,33 @@ <p> BED information should not be mixed as explained above (BED3 should not be mixed with BED4), rather additional column information must be filled for consistency, for example with a "." in some circumstances, if the field content is to be empty. BED fields in custom tracks can be whitespace-delimited or tab-delimited. Only some variations of BED types, such as <a href="../FAQ/FAQformat.html#format1.7">bedDetail</a>, require a tab character delimitation for the detail columns.</p> <p> Please note that only in custom tracks can the first lines of the file consist of header lines, which begin with the word "browser" or "track" to assist the browser in the display and interpretation of the lines of BED data following the headers. Such annotation track header lines are not permissible in downstream utilities such as bedToBigBed, which convert lines of BED text to indexed binary files. </p> <P> If your data set is BED-like, but it is very large (over 50MB) and you would like to keep it on your -own server, you should use the <a href="../goldenPath/help/bigBed.html">bigBed</a> data format.</p> +own server, you should use the <a href="../goldenPath/help/bigBed.html">bigBed</a> data format. +Read a <a href="https://genome-blog.soe.ucsc.edu/blog/2021/08/03/how-make-a-bigbed-file-part-1/" +target="_blank">blog post</a> for step-by-step instructions.</p> <p> 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