bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index caa60a7d19e..3458da4e761 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -89,31 +89,31 @@ 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 bedDetail, require a tab character delimitation for the detail columns.

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.

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 bigBed data format. -Read a blog post for step-by-step instructions.

The first three required BED fields are:

chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671). Many assemblies also support several different chromosome aliases (e.g. '1' or 'NC_000001.11' in place of 'chr1').
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, however, @@ -266,31 +266,31 @@ position fields should uniquely describe items so that the correct ID and description will be displayed on the details pages.

Example:
This example uses the first 4 columns of BED format, but up to 12 may be used. Click here to view this track in the Genome Browser.
```
track name=HbVar type=bedDetail description="HbVar custom track" db=hg19 visibility=3 url="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?display_format=page&mode=output&id=$$"
 chr11	5246919	5246920	Hb_North_York	2619	Hemoglobin variant
 chr11	5255660	5255661	HBD c.1 G>A	2659	delta0 thalassemia
 chr11	5247945	5247946	Hb Sheffield	2672	Hemoglobin variant
 chr11	5255415	5255416	Hb A2-Lyon	2676	Hemoglobin variant
 chr11	5248234	5248235	Hb Aix-les-Bains	2677	Hemoglobin variant 
```
To see an example of turning a bedDetail custom track into the bigBed -format, see this How to make a bigBed file blog post.

PSL format

PSL lines represent alignments, and are typically taken from files generated by BLAT or psLayout. See the BLAT documentation for more details. PSL data tracks can also be visualized in rearrangement display mode. All of the following fields are required on each data line within a PSL file:
1. matches - Number of bases that match that aren't repeats

PSL format