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ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format
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Extracting Gene Annotations #278

Open tli71193 opened 1 year ago

tli71193 commented 1 year ago

Hi there,

I was browsing around the zoonomia data portal and found this link saying that gene prediction annotations are stored in the hal files.

looking through the documentation it looks like I need to use hal2assemblyHub.py to extract the gene annotations, but I'm a little confused on the documentation.

Given the 242 mammalian hal file, how can I extract the gene annotations for each species in the hal file?

glennhickey commented 1 year ago

HAL does not support the storing of gene anotations. They would be in BED or GFF files. When it says

Data is available for every species in the hal alignment...

It means that for every species in the hal, there is an annotation available (in a different file).

The server's too slow (?) for me to find the exact locations now, but the annotations should be up somewhere, as well as viewable on the browser.