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issue using cache=True in scanpy read #371

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bhoellbacher opened this issue Nov 8, 2024 · 0 comments
Open

issue using cache=True in scanpy read #371

bhoellbacher opened this issue Nov 8, 2024 · 0 comments

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@bhoellbacher
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Within the additional_qc_scsnake notebook bc.Import.read_mtx() uses scanpy.read with cache=True to read in the .h5ad file.
If the filtering parameters (such as besca_standard_n_genes: 10000 ) were changed after first running the pipeline, the cached file does not get updated.
This leads to a mismatch in the number of observations between the cached .h5ad file and the barcodes.tsv file.

Setting cache=False resolves this issue without impacting loading times in a noticeable fashion.

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