Add a new genome to the API

[Boer223]

Hi, Can you help me to add my genome and gene annotation to your public api, and I want to use it to build the epigenome browser for my genome.

Here is my 2bit format genome and gene annotation files: genome: http://205.185.113.78/public/epigenome_browser/Westar/Westar.2bit gene annotation: http://205.185.113.78/public/epigenome_browser/Westar/Westar.gene.mRNA.bed

Thank you!

[lidaof]

HI, @Boer223 sure we can do that. should I use westart as your genome name? do you have more information about this genome assembly?

[Boer223]

@lidaof Yes, it's a cultivar of Brassica napus, but now the genome hasn't been published. I only want to use the API to build my own epigenome browser.

[lidaof]

Hi @Boer223 i understand now, so you only want us add the gene data to our API? we can do that. would you please format your data (Westar.gene.mRNA.bed) to our refbed format ?

[Boer223]

@lidaof Yes, and is there any scripts to format the bed or gff3 format to refbed format?

my gff3 format:

##gff-version 3
chrA01  maker   gene    107668  109795  .   -   .   ID=westarA010000010;Name=westarA010000010
chrA01  maker   mRNA    107668  109795  .   -   .   ID=westarA010000010-mRNA-1;Parent=westarA010000010;Name=westarA010000010
chrA01  maker   exon    109777  109795  .   -   .   ID=westarA010000010-mRNA-1.exon1;Parent=westarA010000010-mRNA-1
chrA01  maker   CDS 109777  109795  .   -   0   ID=cds.westarA010000010-mRNA-1;Parent=westarA010000010-mRNA-1
chrA01  maker   exon    109348  109595  .   -   .   ID=westarA010000010-mRNA-1.exon2;Parent=westarA010000010-mRNA-1
chrA01  maker   CDS 109348  109595  .   -   2   ID=cds.westarA010000010-mRNA-1;Parent=westarA010000010-mRNA-1
chrA01  maker   exon    108347  108410  .   -   .   ID=westarA010000010-mRNA-1.exon3;Parent=westarA010000010-mRNA-1
chrA01  maker   CDS 108347  108410  .   -   0   ID=cds.westarA010000010-mRNA-1;Parent=westarA010000010-mRNA-1
chrA01  maker   exon    107668  107696  .   -   .   ID=westarA010000010-mRNA-1.exon4;Parent=westarA010000010-mRNA-1

my bed format

Uncluster   817348  819562  westarUncluster0000010  0   -
Uncluster   843209  852717  westarUncluster0000020  0   -
Uncluster   1613348 1615395 westarUncluster0000030  0   -

[lidaof]

Hi @Boer223 , yes, we have some scripts here, i guess you can check those with gff in the name. let me know if you need any help.

[Boer223]

Thank you for your scripts! I have converted the gene annotation to refbed format successfully, and it's now here: http://205.185.113.78/public/epigenome_browser/Westar/Westar.gene.refbed

[lidaof]

Hi Xiaobo @Boer223 , the data has been added to our API, you can use this link for a quick testing. when you add the track to your genome, you can add this as the gene track model:

new TrackModel({
        type: "geneAnnotation",
        name: "gene",
        genome: "westar",
    }),

[Boer223]

@lidaof Many thanks for your API. I have built the epigenome browser for my genome successfully.

[lidaof]

@Boer223 you are very welcome, and it looks very nice!