I want to display E.coli BW25113 (GenBank: CP009273.1) strain in UCSC browser. This strain is not listed in http://microbes.ucsc.edu/ browser. How can I display E.coli BW25113 assembly in the browser?
How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?
I found two methods:
- You want to visit this page for instructions for novel assemblies: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs .
- However, before doing that I highly recommend that you check Genome Assembly Hub first: https://genome-test.gi.ucsc.edu/gbdb/hubs/genbank/ . There is a good chance that your genome or strain is listed there. Here is an example of how you can do that. Example specifically shows how you can display E.coli BW25113 strain in the browser.
- Go to NCBI Nucleotide: https://www.ncbi.nlm.nih.gov/nucleotide .
- Enter your strain name:
E.coli BW25113 (GenBank: CP009273.1)
- Find Biosample ID on the page, located under DBLINK:
- Go to GenBank assembly hubs: https://genome-test.gi.ucsc.edu/gbdb/hubs/genbank/ .
- Select bacteria. This will take you to "Bacterial assembly hub" at https://genome-test.gi.ucsc.edu/gbdb/hubs/genbank/bacteria/bacteria.html .
- Look for E. coli hubs. At the time I looked #15-18 contain E. coli strains.
- Click on each hub and search for
SAMN03013572using browser search function (Command+F on macOS). I found my genome in hub #16.
- Click on "common name" in the column-3. This will take you to
https://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/gbdb/hubs/genbank/bacteria/16/hub.txt&genome=GCA_000750555.1_ASM75055v1&position=lastDbPos , where
FindPositionwindow will be populated with your genome Assembly.
- Click on Go. This should take you to the UCSC Genome Browser with your genome assembly.
$\begingroup$ Update: The step-9 is no longer working since UCSC genome browser resources described above were experimental prototype proof of concepts that have since been discontinued according to the Genome Browser Team. Once I find an alternative method, I will post it here. $\endgroup$ Nov 24, 2022 at 1:52
I am not sure if this qualifies as an official answer. I have contacted UCSC bioinformatics team. They were were very kind and told me that they would add any track that was requested by users. After my request, they kindly added the track for E.coli BW25113. If you want your reference tracks to be added you could submit a request at this website: Geneme assembly search and request page.
Then, at the upper right corner click on "Can't find your assembly?" button and submit your request. See the screenshot below from the webpage.