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Gene-BC-UMI whitelist #2

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madnessfish opened this issue Apr 7, 2023 · 1 comment
Open

Gene-BC-UMI whitelist #2

madnessfish opened this issue Apr 7, 2023 · 1 comment

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@madnessfish
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Thank you for such an excellent protocol and tools! I learned a lot from your publication. :)
I would like to learn more about how the barcode and UMI are being determined in barcodeUMI_finder_11mer.py.

May I know how can we obtain the "Gene-BC-UMI whitelist from 10x data". Or what format does it looks like?
@noush-joglekar
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Hey there, this script should help you extract the Gene-BC-UMI list from the 10x short read data. It takes in the "molecule_info.h5" as input. Let me know if you have trouble running it

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@madnessfish @noush-joglekar