5357f43c35e9cfb7bb2fae897eab6286954865c1 ccpowell Wed Jul 10 11:33:53 2019 -0700 Switching MySQL to MariaDB where appropriate in the documentation, refs #23597 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index b3da146..2207861 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -213,31 +213,31 @@ the Gateway page to open up the Genome Browser with the annotation track displayed.

The Genome Browser also provides a collection of custom annotation tracks contributed by the UCSC Genome Bioinformatics group and the research community.

NOTE: If an annotation track does not display correctly when you attempt to upload it, you may need to reset the Genome Browser to its default settings, then reload the track. For information on troubleshooting display problems with custom annotation tracks, refer to the troubleshooting section in the Creating custom annotation tracks section.

Viewing genome data as text

The Table Browser, a portal to the underlying -open source MySQL relational database driving the +open source MariaDB relational database driving the Genome Browser, displays genomic data as columns of text rather than as graphical tracks. For more information on using the Table Browser, see the section Getting started: on the Table Browser.

Opening the Genome Browser from external gateways

Several external gateways provide direct links into the Genome Browser. Examples include: Entrez Gene, AceView, Ensembl, SuperFamily, and GeneCards. Journal articles can also link to the browser and provide custom tracks. Be sure to use the assembly date appropriate to the provided coordinates when using data from a journal source.

@@ -1339,33 +1339,33 @@

xenoMrna.zip: All GenBank mRNAs from species other than that of the selected one.

Chromosomes contains the assembled sequence for the genome in separate files for each chromosome in a zipped fasta format. The main assembly can be found in the chrN.fa files, where N is the name of the chromosome. The chrN_random.fa files contain clones that are not yet finished or cannot be placed with certainty at a specific place on the chromosome. In some cases, the chrN_random.fa files also contain haplotypes that differ from the main assembly.

Database contains all of the positional and non-positional tables in the genome annotation database. Each table is represented by 2 files:

.sql file: the MySQL commands used to create the table.
.sql file: the SQL commands used to create the table.
- .txt.gz file: the MySQL database table data in tab-delimited format and + .txt.gz file: the MariaDB database table data in tab-delimited format and compressed with gzip.

Schema descriptions for all tables in the genome annotation database may be viewed by using the "describe table schema" button in the Table Browser.

Cross-species alignments directories, such as the vsMm4 and humorMm3Rn3 directories in the hg16 assembly, contain pairwise and multiple species alignments and filtered alignment files used to produce cross-species annotations. For more information, refer to the READMEs in these directories and the description of the Multiple Alignment Format (MAF).