Open nbartonicek opened 5 years ago
Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu
On Thu, Sep 5, 2019 at 4:18 AM nbartonicek notifications@github.com wrote:
Good day,
I'm receiving a huge proportion of doublets from the same sample under the "BEST" column in demuxlet results.
I've combined bam files from two single-cell experiments (lets call them Sample1 and Sample2) for which we have genotyping data. The majority of cells are assigned as "DBL-Sample1-Sample1" or "AMB-Sample1-Sample1-Sample1". The top singlet (SNG.1ST) corresponds to the right sample in 99% of the cases.
What is the cause of the DBL-Sample1-Sample1 calls and is there a way to circumvent this?
Any help greatly appreciated.
Nenad
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Solved: there was a problem with the alpha parameter. Instead of defining it twice, once as 0 and once as 0.5 I only set it as 0.5. Thanks for your prompt reply though!
Good day,
I'm receiving a huge proportion of doublets from the same sample under the "BEST" column in demuxlet results.
I've combined bam files from two single-cell experiments (lets call them Sample1 and Sample2) for which we have genotyping data. The majority of cells are assigned as "DBL-Sample1-Sample1" or "AMB-Sample1-Sample1-Sample1". The top singlet (SNG.1ST) corresponds to the right sample in 99% of the cases.
What is the cause of the DBL-Sample1-Sample1 calls and is there a way to circumvent this?
Any help greatly appreciated.
Nenad