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rna_genes less genes than the input data #7

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EsperanzaDai opened this issue Oct 27, 2021 · 1 comment
Open

rna_genes less genes than the input data #7

EsperanzaDai opened this issue Oct 27, 2021 · 1 comment
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@wukevin

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@EsperanzaDai
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Hi Kevin,

I have trained a model with ./bin/train_model.py codes and raised the flag --nofilter. However, in the rna_genes.txt, I have 944 genes lost. And I checked the source code in the train_model.py and could not find the exact place where genes are filtered. Could you kindly inform me how those genes are filtered?

Thanks a lot!
Yam
@wukevin
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wukevin commented Nov 15, 2021

Hi Yam - this shouldn't be happening. Can you pleas share the exact command you used (no need to share the files if you aren't comfortable doing that) and the log messages? This should help us narrow down what is happening.

Also, as a sanity check, are these 944 genes all cases where there is 0 expression across all cells in your data?

@wukevin wukevin self-assigned this Nov 15, 2021
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@wukevin @EsperanzaDai