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czbiohub-sf / tabula-sapiens

Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
BSD 3-Clause "New" or "Revised" License
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Smartseq2 annotations? #40

Closed maximilianh closed 1 year ago

maximilianh commented 1 year ago

Is there an explanation somewhere why the cell-type annotation in the H5AD for the Smartseq2 data are missing 2/3 of the cells? Thanks! Max

maximilianh commented 1 year ago

closing this. I reached out to Bob Jones and the number wasn't 2/3 but rather 20% and there are very good explanations why some cells were filtered (only ERCCs, low quality cells)

maximilianh commented 1 year ago

So 20% of the BAM files that are not used in the H5AD are entirely expected.