custom reference genome and annotation support

[sbgonenc]

Hi!
I was wondering if there wold be support for custom genome fasta and annotation files? I see that every genome is hard coded and seems impossible to use my own genome version. Is there a work on progress for that, or would you recommend any work around for it?

Sincere regards,

[ejarmand]

Hi sbgonenc, Snapatac2 does support any fasta/genome annotation! (assuming it's gtf or gff format)

import snapatac2 as snap
myCustomGenome = snap.genome.Genome(fasta='/path/to/your/fasta.fasta', annotation='path/to/your/annotation.gtf')

If you follow the tutorials you can use your custom genome any place you would include snap.genome.hg38, e.g.:

data = snap.pp.import_fragments(
    fragment_file,
    chrom_sizes=myCustomGenome,
    file="pbmc.h5ad",  # Optional
    sorted_by_barcode=False,
)

snap.metrics.tsse(data, myCustomGenome)