alevin: the --whitelist flag

[eudoraleer]

Hi,

I saw this flag on salmon alevin:

I wonder does it mean we cannot use 10x whitelist as input to this flag?

Thanks!

[k3yavi]

Hi @eudoraleer ,

Thanks for checking. That's correct, this flag is for providing a small list of cellular barcodes which you'd like to quantify. A general use case is re-quantification of the Cellranger (or any tool) quantified data and user knows what high quality of barcodes (typically in ~10k) needs to quantified. Alevin will take the list and quantify only the provided barcodes, post cellular barcode correction.

[eudoraleer]

Hi!

Thank you for your quick reply. Does Alevin does barcode correction without user specifying input to this --whitelist flag?

Also, just a quick question, how about 10XV3 whitelist as input to --whitelist flag? Or this whitelist flag is not used for this purpose? Thanks for explaining, I am a bit confused.