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jsxlei / SCALE

Single-cell ATAC-seq analysis via Latent feature Extraction
MIT License
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No output for --binary #21

Open salbrec opened 2 years ago

salbrec commented 2 years ago

Dear Lei, I recently encountered a problem regarding the imputation. I used SCALE already some time ago and I remember I could get data about imputation using the --binary flag (basically I don't need numerical imputed data) which was working back then. However, when I ran SCALE yesterday, I got no imputed output. Everything else seems to be just fine, just the "binary_imputed" folder is missing. More information can be taken from the picture I added. Might be also important: When I first used SCALE it was (I guess) still in the year of publication and in the meanwhile I pulled the most recent version. Can you please check if there is a bug or a wrong usage from my side? Thanks in advance! Steffen

no_imputed

jsxlei commented 2 years ago

Hi Steffen, SCALE has been updated for supporting scanpy that all results are saved in h5ad format file. You should find the binary imputed output in adata.obsm['binary'] after reading the output file adata.h5ad using read_h5ad function in scanpy. Lei

salbrec commented 2 years ago

Hi Lei, thanks for the quick reply! The h5ad format was new to me, however, it was straight forward to get the "binary". As far as I could see, the "impute" output is also there, even though I didn't use the --impute flag. After the update, are those imputation flags true by default? Thanks again, Steffen

jsxlei commented 2 years ago

Hi Steffen, the 'binary' is obtained after calculating the 'impute' in SCALE, I can del 'impute' if you don't need it. To get a 'binary' without 'impute', you just need to git clone the newest rep and install it again (not via pip). Lei