search

zhoux85 / STAligner

STAligner is a tool for alignment and integration of spatially resolved transcriptomics data.
MIT License
29 stars 5 forks source link

Inconsistency in tutorial workflows #27

Closed t-a-m-i closed 4 days ago

t-a-m-i commented 5 days ago

Hi, great package you developed!

I´m currently running some tutorials to make sure my environment setup worked properly and to understand your workflow. I´m just a bit confused about why you do HVGs -> normalize -> log1p in tutorial2 and normalize -> log1p -> HVGs in tutorial4. Could you please elaborate on that a bit?

As far as I understand from the documentation of scanpy, generally logarithmized data is expected for HVGs, except when flavor='seurat_v3'/'seurat_v3_paper', in which count data is expected. (https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.highly_variable_genes.html) Am I missing something crucial? Thanks!

zhoux85 commented 4 days ago

Hi. Please follow the sequence from the documentation of scanpy: normalize -> log1p -> HVGs. I think both workflow works and the results don't make much difference.