Adding option to report UMI barcode in _reads_barcodes.txt output file?

DavidsonGroup / flexiplex

The Flexible Demultiplexer

https://davidsongroup.github.io/flexiplex/

MIT License

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Adding option to report UMI barcode in _reads_barcodes.txt output file? #9

Closed shuyi-w closed 10 months ago

shuyi-w commented 1 year ago

Hello,

Would it be possible to add a way to report the cell barcode and UMI barcode for discovery mode?

Thanks!

olliecheng commented 10 months ago

The recommended approach is to use a separate barcode cleanup tool (such as flexiplex-filter, documented on the website). This is because there is typically a high error rate in the raw barcode data which needs to be cleaned up to be usable. If you really need UMI-barcode pairs with no filtering, you can run another pass of flexiplex on the barcode list with an error tolerance of 0.