muon.atac.tl.locate_genome
muon.atac.tl.locate_genome#
- muon.atac.tl.locate_genome(data: Union[anndata._core.anndata.AnnData, mudata._core.mudata.MuData], fasta_file: str)#
Add path to the FASTA file with genome to .uns[“files”][“genome”]
Genome sequences can be downloaded from GENCODE:
GRCh38: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.p13.genome.fa.gz
GRCm38: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/GRCm38.p6.genome.fa.gz
- Parameters
data – AnnData object with peak counts or multimodal MuData object with ‘atac’ modality.
fasta_file – A path to the file (e.g. ./atac_fragments.tsv.gz).