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Using header=None reads the first line (which is a header) as a row in the gene annotation dataframe. This subsequently affects the dimensions of the whole dataset.
Using
header=None
reads the first line (which is a header) as a row in the gene annotation dataframe. This subsequently affects the dimensions of the whole dataset.https://github.com/sanderlab/scPerturb/blob/fac49ee392f6873b50fad27550e82f6507158834/dataset_processing/SrivatsanTrapnell2020.py#L77C19-L78
Currently, sciPlex3's
var
looks like this:So all the genes are shifted somehow. This can drastically affect downstream tasks since it's no longer clear what genes are expressed.
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