bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html index 18521bfd542..b0dc6588d8c 100755 --- src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html +++ src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html @@ -1,25 +1,25 @@

Assembly

Please note, if you are working with a genome that has already been submitted to the NCBI Assembly system, it may already be available in the UCSC Genome Browser.

Please examine the GenArk Assembly Hub collection to see if your genome of interest is already available. In the case it cannot be found there, you can use the UCSC Assembly Request page to request a genome assembly be added to the UCSC Genome Browser. +

Overview

Web Server

Building Tracks

Cyotoband Track
The trackDb refers to a file which defines the tracks to place on this genome assembly. The format of this file is described in the Track Hub help reference documentation.
The groups refers to a file which defines the track groups on this genome browser. Track groups are the sections of related tracks grouped together under the primary genome browser graphics display image.
The description will be displayed for user information on the gateway page and most title pages of this genome assembly browser. It is the name displayed in the assembly pull-down menu on the browser gateway page.
The twoBitPath refers to the .2bit file containing the sequence for this assembly. Typically this file is constructed from the original fasta files for the sequence using the kent program faToTwoBit. This line can also point to a URL, for example, if you are duplicating an existing Assembly Hub, you can use the original hub's 2bit file's URL location here.
The organism string is displayed along with the description on most title pages in the genome browser. Adjust your names in organism and description until they are appropriate. This example is very close to what the genome browser normally displays. This organism name is the name that appears in the genome pull-down menu on the browser gateway page.
The defaultPos specifies the default position the genome browser will open when a user first views this assembly. This is usually selected to highlight a popular gene or region of interest in the genome assembly.
The orderKey is used with other genome definitions at this hub to order the pull-down menu ordering the genome pull-down menu.
The htmlPath refers to an html file that is used on the gateway page to display information about the assembly.
The transBlat, blat, and isPcr entries refer to different configurations of the gfServer that enhance search capabilities for amino acids, BLAT algorithms, and PCR respectively. More here.

Note that it is strongly encouraged to give each of your genomes stanza's a line for defaultPos, scientificName, organism, description (along with other above settings) so that when your hub is attached it will load a specified default location and have text to be more easily searched from the Gateway page.

2bit File

- The .2bit file is constructed from the fasta sequence for the assembly. The kent source program faToTwoBit is used to construct this file. Download the program from the downloads section of the Browser. For example: + The .2bit file is constructed from the fasta sequence for the assembly. The kent source program faToTwoBit is used to construct this file. Download the program from the downloads section of the Browser. For example:

 faToTwoBit ricCom1.fa ricCom1.2bit

Use the twoBitInfo to verify the sequences in this assembly and create a chrom.sizes file which is not used in the hub, but is useful in later processing to construct the big* files:

 twoBitInfo ricCom1.2bit stdout | sort -k2rn > ricCom1.chrom.sizes

The .2bit commands can function with the .2bit file at a URL: