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bigWig files

bigWig files store genomic data in a compressed, indexed form that allows rapid retrieval and visualization. bigWig files can be loaded directly into HiGlass using the vector datatype and bigwig filetype:

docker exec higlass-container python \
        higlass-server/manage.py ingest_tileset \
        --filename /tmp/cnvs_hw.bigWig \
        --filetype bigwig \
        --datatype vector \
        --coordSystem hg19

Important: BigWig 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 bigWig file in ingest_tileset, HiGlass will try to find one in the database that matches the chromosomes present in the bigWig file. If a chromsizes tileset is found, it's coordSystem will also be used for the bigWig 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 bigWig, but no chromsizes are found on the server, the import will fail.

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

ingest_tileset --filetype chromsizes-tsv --datatype chromsizes --coordSystem hg19 --filename chromSizes.tsv

and then to add the bigWig with the same coordSystem:

ingest_tileset --filetype bigwig --datatype vector --coordSystem hg19 --filename cnvs_hw.bigWig