Hi, this looks to be a wonderful tool - thank you for making this for the community!
Our group is working with single-nuclear samples from solid organs and we're interested in minimizing costs via multiplexing. We've typically noted more contamination with nuclear preps compared to single-cell preps (e.g., for PBMC analysis). With that in mind, I was curious about the reliability of the posterior probability calculations produced by demuxlet, as the original paper and most other literature I've come across where demuxlet was used were in the context of single-cell preps.
I have read the nuclei multiplexing paper from Aviv Regev's group (https://www.nature.com/articles/s41467-019-10756-2), as they used demuxlet as a comparison for their DemuxEM tool. However, I was interested in getting your opinion on any modifications that should be done, etc, if we wanted to use genotyping and demuxlet for our analyses. Thanks!
Hi, this looks to be a wonderful tool - thank you for making this for the community!
Our group is working with single-nuclear samples from solid organs and we're interested in minimizing costs via multiplexing. We've typically noted more contamination with nuclear preps compared to single-cell preps (e.g., for PBMC analysis). With that in mind, I was curious about the reliability of the posterior probability calculations produced by demuxlet, as the original paper and most other literature I've come across where demuxlet was used were in the context of single-cell preps.
I have read the nuclei multiplexing paper from Aviv Regev's group (https://www.nature.com/articles/s41467-019-10756-2), as they used demuxlet as a comparison for their DemuxEM tool. However, I was interested in getting your opinion on any modifications that should be done, etc, if we wanted to use genotyping and demuxlet for our analyses. Thanks!