Dear WashU Epigenome Browser Developers,
First of all, thank you very much for developing and maintaining such a wonderful and powerful genome browser ecosystem.
I am currently working on a cross-species comparative epigenomics project involving two non-model mammalian species. Neither of these genome assemblies exists in the built-in species repository.
I have set up local data hosting via Nginx (providing 2bit genomes, bigWig tracks, indexed refBed gene annotations, and genomealign / weaver tracks processed from AXT alignments). While single-genome custom hubs work perfectly, I am encountering critical challenges when attempting to configure a Comparative View between two non-model/custom genomes using custom JSON hubs.
The Challenges / Bugs Encountered:
0 tracks issue for Query Genome:
When defining both non-model genomes in a single Multi-Genome DataHub JSON array and configuring a genomealign track under defaultTracks, the browser successfully detects and displays the query genome container in the Tracks panel. However, it displays 0 tracks under the query genome, preventing any tracks or split-view windows for the query genome from being rendered.
Lack of Clear Specification for Comparative Custom Hubs:
Most available documentation and Session JSON examples for Comparative View rely on standard/built-in assemblies (e.g., hg19 vs mm10). There seems to be a lack of standard documentation/schema on how to properly construct a standalone DataHub JSON that binds two entirely custom, non-built-in genomes together with active alignment ribbons.
Questions / Request for Guidance:
What is the recommended or officially supported JSON DataHub structure for initializing a Comparative View between two custom genomes (neither of which is pre-registered in WashU's backend)?
How should the genomealign track be structured so that the browser automatically loads and renders tracks for both the Primary and Query custom genomes simultaneously upon Hub loading?
I would greatly appreciate any code examples, JSON schemas, or troubleshooting suggestions on how to achieve this!
Best regards
Dear WashU Epigenome Browser Developers,
First of all, thank you very much for developing and maintaining such a wonderful and powerful genome browser ecosystem.
I am currently working on a cross-species comparative epigenomics project involving two non-model mammalian species. Neither of these genome assemblies exists in the built-in species repository.
I have set up local data hosting via Nginx (providing 2bit genomes, bigWig tracks, indexed refBed gene annotations, and genomealign / weaver tracks processed from AXT alignments). While single-genome custom hubs work perfectly, I am encountering critical challenges when attempting to configure a Comparative View between two non-model/custom genomes using custom JSON hubs.
The Challenges / Bugs Encountered:
0 tracks issue for Query Genome:
When defining both non-model genomes in a single Multi-Genome DataHub JSON array and configuring a genomealign track under defaultTracks, the browser successfully detects and displays the query genome container in the Tracks panel. However, it displays 0 tracks under the query genome, preventing any tracks or split-view windows for the query genome from being rendered.
Lack of Clear Specification for Comparative Custom Hubs:
Most available documentation and Session JSON examples for Comparative View rely on standard/built-in assemblies (e.g., hg19 vs mm10). There seems to be a lack of standard documentation/schema on how to properly construct a standalone DataHub JSON that binds two entirely custom, non-built-in genomes together with active alignment ribbons.
Questions / Request for Guidance:
What is the recommended or officially supported JSON DataHub structure for initializing a Comparative View between two custom genomes (neither of which is pre-registered in WashU's backend)?
How should the genomealign track be structured so that the browser automatically loads and renders tracks for both the Primary and Query custom genomes simultaneously upon Hub loading?
I would greatly appreciate any code examples, JSON schemas, or troubleshooting suggestions on how to achieve this!
Best regards