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It appears that in the cell ranger code, the dispersion is calculated using the negative binomial relationship between mean and dispersion, see
https://github.com/10XGenomics/cellranger/blob/5f5a62…
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### Name of the tool
CellRanger ARC
### Tool homepage
https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
### Tool description
Add comp…
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Hello,
I've recently tried to "replicate" cellranger analysis by running STAR solo and then empty drops on the unfiltered data. STAR solo gives me the correct (as in, the same as cellranger 3.0) n…
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Hello!
This is my first time running CellBender and I'm so happy I got it to work! However, when looking over the output files, it seems like I'm missing an output_report.html file. Below is the l…
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I'm trying to replicate Cellranger v3 on a 10x library with version 3 chemistry and getting wildly different cell estimates from the starsolo/emptydrops software. With Starsolo i am running the follow…
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Hi,
I've run cellbender on my data and read the filtered count matrix into R using `Read_CellBender_h5_Mat` from scCustomize and then converted that to a Seurat object using `CreateSeuratObject`.
…
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I noticed starsolo was designed to work in many different platforms of scRNAseq, e.g. 10X/Indrop/SeqWell. However, I don't find the corresponding category for single cell combinatorial indexing RNA …
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Hi,
I am trying to replicate the results you have obtained and I run into a versioning problem.
On the one hand, you use cellranger version 2.1.1. This version by default uses a version of STAR 2.…
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Hello, I've successfully run cellranger-arc for all 10x Multiome samples, but in the .html output ([attached here](https://www.dropbox.com/s/gqrx0i9ipxe24lc/Wang2023_cellranger_html.zip?dl=0)) I get a…
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Why is there a big difference between kallisto and cellranger count result？
sample：
https://www.ncbi.nlm.nih.gov/sra/SRR8315735
kallisto:
![image](https://user-images.githubusercontent.com/3…