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/makeDb/trackDb/human/hg38/rmsk.html src/hg/makeDb/trackDb/human/hg38/rmsk.html index 9585377fad0..1166c39e53e 100644 --- src/hg/makeDb/trackDb/human/hg38/rmsk.html +++ src/hg/makeDb/trackDb/human/hg38/rmsk.html @@ -14,31 +14,31 @@ Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below.

This track and the masking information in our hg38 genome download FASTA files was created in 2010 with the original RepBase library from 2010-03-02 and RepeatMasker 3.0.1. Since April 2019, RepBase is under a commercial license, we cannot distribute it or update the track using the RepBase library without a license. Therefore, and for compatibility with past results, given how central the masking is for many other annotations, we decided to not update the repeatmasking of hg38. However, you can show the small differences between the RepeatMasker 3/RepBase from 2010 and RepeatMasker 4/DFAM from 2020 using the track "RepeatMasker Viz" in the same track group. It contains two subtracks, one with the old and one with the new data. Also, these -tracks have many more visusalisation options than the original RepeatMasker +tracks have many more visualization options than the original RepeatMasker track.

However, the last track update time of this track at UCSC is not 2010, because we had to add repeatmasking annotations to the rarely used _alt and _fix "patch" sequences of the hg38 genome. The repeatmasking annotations of the main chromosomes were unaffected and have not changed since 2010. For more information on genome patches, see our blog post.

Display Conventions and Configuration

In full display mode, this track displays up to ten different classes of repeats: