depositing VacV genome

[Chorong Park]

Hello,

I would like to ask to deposit human and VacV genome that's combined.

Reference genomes, combining human

genome (Ensembl, GRCh38/hg38) and VacV genome (Genbank: AY243312.1).

I was trying to drop the .fa and .gft file here but it seems like they are too big to drop...

So I assume this is not how I should do it.

Could you please instruct me?

All the best,

Chorong

[Gerardo Perez]

Hello, Chorong.

Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.

We have the ViralProj15241 Vaccinia virus (GCF_000860085.1), along with other virus genomes, available as genome browsers:
https://hgdownload.soe.ucsc.edu/hubs/viral/index.html

The ViralProj15241 Vaccinia virus (GCF_000860085.1) can be viewed directly at the following link:
https://genome.ucsc.edu/h/GCF_000860085.1

You can visualize your assembly using our Assembly Hub feature and upload your GTF file as a custom track. Assembly hubs allow users to host their genomes and related annotations on a publicly accessible web server, and then use the UCSC Genome Browser to visualize these annotations. You can find information about creating assembly hubs on the following help pages:

• Quick Start Guide to Assembly Hubs (https://genome.ucsc.edu/goldenPath/help/hubQuickStartAssembly.html)
• Assembly Hub wiki (http://genomewiki.ucsc.edu/index.php/Assembly_Hubs)

Example Assembly Hub

You can explore this working example for reference:
hub.txt for ViralProj15241 Vaccinia virus: https://hgdownload.soe.ucsc.edu/hubs/GCF/000/860/085/GCF_000860085.1/hub.txt

It includes the essential components:

hub.txt

hub GCF_000860085.1 genome assembly
shortLabel Vaccinia virus (WR (Western Reserve) 2005)
longLabel Vaccinia virus (WR (Western Reserve) 2005)/Orthopoxvirus vaccinia/GCF_000860085.1_ViralProj15241 genome assembly
useOneFile on
descriptionUrl html/GCF_000860085.1_ViralProj15241.description.html

genomes.txt

genome GCF_000860085.1
groups groups.txt
description Vaccinia virus (WR (Western Reserve) 2005)
twoBitPath GCF_000860085.1.2bit
chromSizes GCF_000860085.1.chrom.sizes.txt
organism ViralProj15241 May 2005
defaultPos NC_006998.1:64903-74903
scientificName Orthopoxvirus vaccinia
htmlPath html/GCF_000860085.1_ViralProj15241.description.html

Example trackDb.txt sections

track assembly
longLabel Assembly
shortLabel Assembly
visibility hide
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCF_000860085.1_ViralProj15241.assembly.bb
type bigBed 6
html html/GCF_000860085.1_ViralProj15241.assembly
searchIndex name
searchTrix ixIxx/GCF_000860085.1_ViralProj15241.assembly.ix
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map

track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility dense
autoScale Off
maxHeightPixels 128:36:16
graphTypeDefault Bar
gridDefault OFF
windowingFunction Mean
color 0,0,0
altColor 128,128,128
viewLimits 30:70
type bigWig 0 100
bigDataUrl bbi/GCF_000860085.1_ViralProj15241.gc5Base.bw
html html/GCF_000860085.1_ViralProj15241.gc5Base

Displaying the Assembly Hub by Default on a UCSC Mirror

If you are hosting your own UCSC Genome Browser mirror, you can configure it to show your assembly hub by default:

1. Make a session (http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html) in your mirror with the assembly displayed on the browser graphic and save the session with the name ‘session_settings’.

2. Open shell on your mirror: ssh mirror.

3. In a writable directory, create a file named defaultCart.sql with the following content:

#The default cart
CREATE TABLE defaultCart (
    contents longblob not null    # cart contents
);

4. Drop the existing defaultCart table by running the following query:

mysql hgcentral -Ne "DROP TABLE defaultCart" 

5. Load the defaultCart.sql file as a table by running the following query:

mysql hgcentral < defaultCart.sql

6. Insert your session to the default cart table by using your user name and the session name, which was the session saved in Step 1, and run the following query (add your userName):

mysql hgcentral -Ne "insert into defaultCart select contents from namedSessionDb where sessionName='nameOfSession' and userName='nameOfUser'" 

After setup, the hub will load automatically each time you open your mirror, even after a reset.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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