Closed Boer223 closed 2 years ago
HI, @Boer223 sure we can do that. should I use westart
as your genome name? do you have more information about this genome assembly?
@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.
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 ?
@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 -
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.
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
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",
}),
@lidaof Many thanks for your API. I have built the epigenome browser for my genome successfully.
@Boer223 you are very welcome, and it looks very nice!
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!