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ebi-gene-expression-group / scanpy-scripts

Scripts for using scanpy
Apache License 2.0
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0.0.5: read_10x var names not being picked up #46

Closed pcm32 closed 5 years ago

pcm32 commented 5 years ago

Even though -v gene_ids is set, the resulting anndata object is in gene_symbols mode:

image

this produces that our gene symbols on the second column of the genes files don't get incorporated in the anndata object, losing gene symbols.

nh3 commented 5 years ago

-v gene_ids means the 1st column "gene_ids" is used as index for the var table, leaving "gene_symbols" as the only column. If -v gene_symbols is given, the 2nd column "gene_symbols" is used as index and leaving "gene_ids" as the only column. This is the expected behaviour. No information is lost.