If I have example genome sequence (3GB) around 4000 contig. And maximum contig length is 15Mbp.
Also, I have bed file for HG19.
Could someone know how to transfer HG19 annotation (from bed file) to a genome sequence? (Also recommend alignment tools)
For example, I have HG19 KIR region annotation, If I aligned HG19 to genome sequence, I can see where is located KIR region in the genome sequence from HG19 annotation. And I believe there is some way I can copy this annotation to genome sequence and this genome sequence can be a reference. For instance, I know where KIR region is located in the genome sequence, I can easily extract sequence from annotation bed file.
Thank you,
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clear.choi •
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This is going to need a lot more explanation - I honestly cannot fathom what you're talking about. There is the reference genome, a bed file with annotation, and details on some kind of "contigs". There is also talk of an "example" genome. What's going on here?
EDIT: It's a little clearer now. You have a bed file with annotations for hg19 and you'd like to align your sequences to hg19. These are two independent entities that do not need to be conflated. Your hg19 annotation file will be valid as long as your sequences are from the human genome. hg19 is the reference genome, and any annotation (any co-ordinate based bed-format annotation) applicable to hg19 will be applicable as-is to anything that you'd logically align to hg19, unless you're talking large scale (gene-level) structural changes.