198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/hgTablesHelp.html src/hg/htdocs/goldenPath/help/hgTablesHelp.html index c9297430b0d..1c4d1947f06 100755 --- src/hg/htdocs/goldenPath/help/hgTablesHelp.html +++ src/hg/htdocs/goldenPath/help/hgTablesHelp.html @@ -83,31 +83,31 @@ The Table Browser provides a powerful and flexible graphical interface for querying and manipulating the Genome Browser annotation tables. Because the Table Browser uses the same database as the Genome Browser, the two views are always consistent.

Using the Table Browser, you can:

retrieve the DNA sequence data or annotation data underlying Genome Browser tracks for the entire genome, a specified coordinate range, or a set of accessions
apply a filter to set constraints on field values included in the output
generate a custom track and automatically add it to your session so that it can be graphically displayed in the Genome Browser
- conduct both structured and free-from SQL queries on the data
combine queries on multiple tables or custom tracks through an intersection or union and generate a single set of output data
display basic statistics calculated over a selected data set
display the schema for table and list all other tables in the database connected to the table
organize the output data into several different formats for use in other applications, spreadsheets, or databases

This User's Guide is aimed at both the novice Table Browser user as well the advanced user. If you are new to the Table Browser, read the Getting started section to learn about browser basics and try some simple queries. Advanced users may want to proceed directly to the section that addresses a particular area of functionality in detail.

@@ -573,31 +573,31 @@ base-by-base comparisons examine the primary table and the table underlying the secondary track one base at a time. The structure of the primary table is not preserved in this comparison. For example, even if the primary table describes exon structure, the intersection results will contain only position ranges; no information about exon/block structure, strand, or translation region will be retained.

Click the circle in front of a combination method to select it. Only one method may be selected from the two sets of methods. For more information about the individual combination options, see the Intersection Options section.

Step 5. (optional) Select the complement options
Check the box in front of one or both tables to complement the feature data. The complement options allow you to invert the set of positions covered by one or both tables. For example, if you -choose to complement the primary track, any position covered by the that track's features will be +choose to complement the primary track, any position covered by that track's features will be considered not covered, and vice versa. This option provides more flexibility in comparing track positions.

Step 6. Click the Submit button to apply the intersection
Once an intersection has been created on a table, it will persist for the duration of the Table Browser session or until it has been cleared. Only one intersection may exist at a time. To modify an existing intersection, click the Edit button on the intersection line. To remove an intersection, click the Clear button.

Intersecting data from more than two tables

The Table Browser intersection utility limits combinations to only two tables. An existing intersection may be expanded to include additional tables by using the Table @@ -632,31 +632,31 @@ (unless you choose an output format in which the structure is lost). Primary table features are kept or discarded based on the amount of positional overlap with the features in the table underlying the secondary track. The Table Browser offers the following options in this category:

Any overlap: A primary table record will appear in the output if any of its base positions are covered by any feature in the secondary table.
No overlap: A primary table record will appear in the output only if none of its base positions are covered by any feature in the secondary table.
Overlap greater than a specified threshold: A primary table record will appear in the output if the percentage of its base positions covered by secondary table features is greater than the user-specified threshold.
- Overlap less a specified threshold: A primary table record will appear in the + Overlap less than a specified threshold: A primary table record will appear in the output if the percentage of its base positions covered by secondary table features is less than the user-specified threshold.

Note: If the primary table has an exon/block structure, only those bases located in exons and/or blocks will be counted.

Base-by-base comparisons
In these combination options, the positions of the primary and secondary table features are compared one base position at a time. When applying base-by-base comparisons, the structure of the primary table is not preserved. For example, if the refGene table (from the human RefSeq Genes track) is compared with a secondary table using these comparisons, the resulting output data will not describe exon structure. Instead, only position ranges will be returned; the exon/block structure, strand, and translation region information will be discarded. The Table Browser provides the following base-by-base combination options: