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what strategy is applied to select CB #107

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YOU-k opened this issue Jun 3, 2020 · 1 comment
Open

what strategy is applied to select CB #107

YOU-k opened this issue Jun 3, 2020 · 1 comment

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@YOU-k
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YOU-k commented Jun 3, 2020

Hi, I both ran dropseqpipe and Cellranger with emptydrops, but i just find that the cells selected quite differ. I would like to know what exactly you applied to select true cells from ambient RNA.
Thanks!
@Hoohm
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Hoohm commented Jun 24, 2020

Hey @YOU-k
Our filters are based on either a provided whitelist or on the number of cells provided in the sample.csv file.

We don't perform any selection based on expression values for example. We prefer letting the user decide so that we don't skew the data as consensus on filtering is not totally stable yet.

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@Hoohm @YOU-k