Hello - I’m a novice with multimodal analysis, but relatively comfortable with scanpy. I have a scATAC dataset (GEO Accession viewer) that I’m trying to pair with another scRNA dataset, but I’m having trouble loading the ATAC dataset with
Here is the data in question:
# Download the RAW file from the output above ftp_link = r'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE182nnn/GSE182134/suppl/GSE182134_RAW.tar' ! curl -O $ftp_link
After unzipping, I get the following files
./E11_5rep1/ ./E11_5rep1/fragments.tsv.gz.tbi ./E11_5rep1/singlecell.csv ./E11_5rep1/fragments.tsv.gz
etc. … - I’ve tried using
muon.read_10x_mtx(path_) , where
path_ = r'/content/E11_5rep1/' but the error:
FileNotFoundError: Did not find file /content/E11_5rep1/matrix.mtx.gz.
… and not sure how to troubleshoot from there - any help is appreciated!