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bigBed files

bigBed files store genomic annotation data (particularly exons) in an optionally compressed, indexed form that allows rapid retrieval and visualization. bigBed files can be loaded directly into HiGlass using the gene-bed12-annotation datatype and bigbed filetype:

docker exec higlass-container python \
        higlass-server/manage.py ingest_tileset \
        --filename /tmp/annotations.bigBed \
        --filetype bigbed \
        --datatype gene-bed12-annotation \
        --coordSystem hg38

Important: BigBed files have to be associated with a chromosome order!! This means that there needs to be a chromsizes file for the specified assembly (coordSystem) in the higlass database. If no coordSystem is specified for the bigBed file in ingest_tileset, HiGlass will try to find one in the database that matches the chromosomes present in the bigBed file. If a chromsizes tileset is found, it's coordSystem will also be used for the bigBed file. If none are found, the import will fail. If more than one is found, the import will also fail. If a coordSystem is specified for the bigBed, but no chromsizes are found on the server, the import will fail.

TLDR: The simplest way to import a bigBed is to have a chromsizes present e.g.

ingest_tileset --filetype chromsizes-tsv --datatype chromsizes --coordSystem hg38 --filename chromSizes.hg38.tsv

and then to add the bigBed with the same coordSystem:

ingest_tileset --filetype bigbed --datatype gene-bed12-annotation --coordSystem hg38 --filename annotations.bigBed