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Teichlab / cellphonedb

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Are counts filtered? #272

Closed suhasaii closed 3 years ago

suhasaii commented 3 years ago

I am using scRNA data with hgnc_genesymbols and count data as a input to cellphonedb. It gives error at validation "All counts filtered: Are you using human data?"

Screen Shot 2021-02-23 at 1 23 04 PM

issue1

simon7073 commented 3 years ago

Hi, something might be helpful. From #18 .

CellPhoneDB works only with human ensembl ids, that's why all the genes are filtered out. You would need to convert the gene names into ensembl ids and input that into the method.

OR

Did you use the parameter --counts-data=gene_name when you run it?

Best, suhasaii

prete commented 3 years ago

@suhasaii did you manage to run it using --counts-data=gene_name ?

prete commented 3 years ago

Closed due to inactiviity.

"All counts filtered: Are you using human data?" usually refers to either a wrong counts file format or using the wrong gene identifier (default is ensembl but can be changed to HGNC using the --counts-data option.)