The .2bit commands can function with the .2bit file at a URL:
twoBitInfo -udcDir=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/ricCom1.2bit stdout | sort -k2nr > ricCom1.chrom.sizes
Sequence can be extracted from the .2bit file with the twoBitToFa command, for example:
twoBitToFa -seq=chrCp -udcDir=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/ricCom1.2bit stdout > ricCom1.chrCp.fa
The groups.txt file defines the grouping of track controls under the primary genome browser image display. The example referenced here has the usual definitions as found in the UCSC Genome Browser.
+The groups.txt file defines the grouping of track controls under the primary genome browser image display. The example referenced here has the usual definitions as found in the UCSC Genome Browser.
Each group is defined, for example the Mapping group:
name map label Mapping priority 2 defaultIsClosed 0
For more informations about the syntax of the trackDb.txt file, use UCSC's Hub Track Database Definition page. It helps to have a cluster super computer to process the genomes to construct tracks. It can be done for small genomes on single computers that have multiple cores. The process for each track is unique. Please note the continuing document: Browser Track Construction for a discussion of constructing tracks for your assembly hub.
Assembly hubs can have a Cytoband track that can allow for quicker navigation of individual chromosomes and display banding pattern information if known.
A quick version of the track can be built using the existing chrom.sizes files for your assembly (the banding options include gneg, gpos25, gpos50, gpos75, gpos100, acen, gvar, or stalk):
cat araTha1.chrom.sizes | sort -k1,1 -k2,2n | awk '{print $1,0,$2,$1,"gneg"}' > cytoBandIdeo.bed
The resulting bed file can be turned into a big bed and given a .as file (example here) to inform the browser it is not a normal bed.
bedToBigBed -type=bed4 cytoBandIdeo.bed -as=cytoBand.as araTha1.chrom.sizes cytoBandIdeo.bigBed-
In the trackDb, as long as the track is named cytoBandIdeo (track cytoBandIdeo example) it will load in the assembly hub.
+In the trackDb, as long as the track is named cytoBandIdeo (track cytoBandIdeo) it will load in the assembly hub.
There are resources for automatically building assembly hubs available from G-OnRamp and MakeHub.
There is also a collection of Example NCBI assembly hubs that are already working and can either be used or copied as a template to build further hubs.
- G-OnRamp is a Galaxy workflow that turns a genome assembly and RNA-Seq data into a Genome Browser with multiple evidence tracks. Because G-OnRamp is based on the Galaxy platform, developing some familiarity with the key concepts and functionalities of Galaxy would be beneficial prior to using G-OnRamp. Here is a link to their instruction page that gives an overview of their process. + G-OnRamp is a Galaxy workflow that turns a genome assembly and RNA-Seq data into a Genome Browser with multiple evidence tracks. Because G-OnRamp is based on the Galaxy platform, developing some familiarity with the key concepts and functionalities of Galaxy would be beneficial prior to using G-OnRamp. Visit the G-OnRamp website for an overview of their process.
MakeHub is a command line tool for the fully automatic generation of track data hubs for visualizing genomes with the UCSC genome browser. More information can be found on their GitHub page.
Here are some quick steps to load an example hub from this collection, and an attempt to explain how to look at the files behind the hub.
BLAT servers (gfServer) are configured as either dedicated or dynamic servers. Dedicated BLAT serves index a genome when started and remain running in memory to quickly respond to request. Dynamic BLAT servers pre-index genomes to files and are run on demand to handle a BLAT request and then exit.
Dedicated gfServer are easier to configure and faster to respond. However, the server continually uses memory. A dynamic gfServer is more appropriate with multiple assemblies and infrequent use. Their response time is usually acceptable; however, it varies with the speed of the disk containing the index. With repeated access, the operating system will cache the indexes in memory, improving response time.
By running your own BLAT server, you can add lines to the genomes.txt file of your assembly hub to enable the browser to access the server and activate blat searches.
-Please see Running your own gfServer for details on installing and configuring both dedicated and dynamic gfServers.
+Please see the gfServer documentation for details on installing and configuring both dedicated and dynamic gfServers.
transBlat yourServer.yourInstitution.edu 17777 blat yourServer.yourInstitution.edu 17779 isPcr yourServer.yourInstitution.edu 17779
Please see more about configuring your blat gfServer to replicate the UCSC Browser's settings, which will also have information about optimizing PCR results. The Source Downloads page offers access to utilities with pre-compiled binaries such as gfserver found in a blat/ directory for your machine type here and further blat documentation here, and the gfServer usage statement for further options.
+Please see the gfServer documentation for configuring your blat gfServer to replicate the UCSC Browser's settings, which will also have information about optimizing PCR results. The Source Downloads page offers access to utilities with pre-compiled binaries such as gfserver found in a blat/ directory for your machine type, and the gfServer usage statement for further options.
Please also know you can set up gfservers on docker and run it locally.
Note: You can stop your instance of gfServer with a command. For example:
gfServer stop localhost 17860
You can see this error if you have the translatedBlat / nucleotideBlat port numbers the wrong way around:
Expecting 6 words from server got 2
The following is an example of an error message when attempting to run a DNA sequence query via the web-based BLAT tool after loading a hub, after starting a gfServer instance (from the same dir as the 2bit file). For example, a command to start an instance of gfServer:
gfServer start localhost 17779 -stepSize=5 contigsRenamed.2bit &