Build your genome species page
All data loading is done with galaxy, with tools from the Tripal or Chado menu on the left. Prefer the Chado tools as they usually are faster and more reliable.
For a typical genome, you will do something like this:
Chado > Chado organism add
Genus: Genus
Species: species (”species rice” if you load multiple variants)
Common: The famous invulnerable aphid (or gspecies if there is no common name for this species)
Abbr: G. species (”G. species rice” if you load multiple variants)
Chado > Chado analysis add
Name: Genus species genome v5.0
Program: Assembler program (if you don’t know, write ‘Performed by xxx’)
Programversion: v1.0.0, genome v5.0 (if you don’t know, write at least ‘genome v5.0’)
Sourcename: Your lab (or the lab who made the assembly)
Date Executed: The date of creation of the data (if available)
You can populate other if you have more infomation (like source version or execution date)
Chado > Chado analysis add
Analysis name: Genus species OGS5.0
Program name: Annotation program (if you don’t know, write ‘Performed by xxx’)
Program version: v1.0.0, OGS5.0 (if you don’t know, write at least ‘OGS5.0’)
Source name: Your lab (or the lab who made the assembly)
Date Executed: The date of creation of the data (if available)
You can populate other if you have more infomation (like source version or execution date)
Chado > Chado load fasta to load the genome
Fasta: the genome sequence
Organism: The organism you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Analysis: The “Genus species genome v5.0” analysis you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Sequence type: contig
Leave the rest unchanged
Chado > Chado load gff
Gff: the annotation GFF3 file
Organism: The organism you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Analysis: The “Genus species OGS5.0” analysis you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Landmark type: contig
Proteins naming method: From GFF attribute
Protein id attribute:
IDFasta: the protein sequences
Run this only after the following dataset is ready: the output dataset from previous job
Leave the rest unchanged
Tripal > Synchronize features
Organism: The organism you create above (if it doesn’t appear, wait a few minutes, the list is cached)
Feature types: add 2 items: ‘mRNA’ and ‘polypeptide’
Once this job is finished you should be able to access web pages for loaded mRNAs and polypeptide.
The next step is to load functional annotation.
Tripal > Synchronize an organism
Organism: The organism you create above (if it doesn’t appear, wait a few minutes, the list is cached)
Once this job is finished you should be able to access web pages for loaded mRNAs and polypeptide.
The next step is to load functional annotation.
Tripal > Synchronize an analysis
Analysis: The genome analysis you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Tripal > Synchronize an analysis
Analysis: The annotation analysis you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Chado > Chado analysis add
Analysis name: Blast2GO on OGS5.0
Program name: Blast2GO
Program version: 1.4.4 with 2019.10 database, on OGS5.0
Source name: Your lab
Date Executed: The date of creation of the data (if available)
You can populate other if you have more infomation (like source version or execution date)
Chado > Chado load GO annotation
GO annotation: the gaf file
Analysis: The analysis you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Organism: The organism you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Query type: polypeptide
Skip Missing: Yes
Run this only after the following dataset is ready: the output dataset from previous job
You can populate execution date if you know it.
Chado > Chado analysis add
Analysis name: InterProScan on OGS5.0
Program name: InterProScan
Program version: 5.35-74.0, on OGS5.0
Source name: Your lab
Date Executed: The date of creation of the data (if available)
Chado > Chado load InterProScan results
InterProScan results: the xml file
Analysis: The analysis you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Organism: The organism you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Query type: polypeptide
Run this only after the following dataset is ready: the output dataset from previous job
You can populate execution date if you know it. If you used Blastp:
Chado > Chado analysis add
Analysis name: Blastp: on OGS5.0 vs NR
Program name: Blastp
Program version: 2.6.0, NR 2019-11-29, OGS5.0
Source name: Your lab
Date Executed: The date of creation of the data (if available)
If you used Diamond:
Chado > Chado analysis add
Analysis name: Diamond: on OGS5.0 vs NR
Program name: Diamond
Program version: 0.9.25, NR 2019-11-29, OGS5.0
Source name: Your lab
Date Executed: The date of creation of the data (if available)
When using either diamond or blastp:
Chado > Chado load Blast results
Blast results: the xml file
Analysis: The analysis you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Organism: The organism you created above (if it doesn’t appear, wait a few minutes, the list is cached)
Query type: polypeptide
Database blasted against: Select database in the list
Run this only after the following dataset is ready: the output dataset from previous job
You can populate execution date if you know it.
For each of the blast2go, blastp/diamond and interproscan analyses:
Tripal > Synchronize an analysis
Analysis: The analysis you create above (if it doesn’t appear, wait a few minutes, the list is cached)
Tripal > Populate materialized views
Run this only after the following dataset is ready: the output dataset from previous job
Leave the form unchanged
Tripal > Index Tripal data
Run this only after the following dataset is ready: the output dataset from previous job
Leave the form unchanged