muon.atac.tl.locate_genome

muon.atac.tl.locate_genome(data: AnnData | 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).