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Hi!
I'm getting a crash when running emptyDropsCellRanger.
The call:
```
DropletUtils::emptyDropsCellRanger(dge)
```
Where dge is a matrix of cells by genes. I'll note this data set is comp…
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Hi,
While trying to use this very nice package but I encounter an error apparently due to the bam file I use
I am using cellranger/5.0.1 to generate the bam file
and get the error while running scT…
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Hi there,
I am trying to analyse my single-cell RNA data with the pipeline. I am not very experienced with bioinformatics. I am using the unfiltered bam file and in this experiment I have multiple…
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Initially, I had demultiplexed [Smart-Seq 3 dataset ](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209749) for each cell separately without barcodes.
I concatenated 5 fastq files with [this …
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Hi,
I am very excited that there finally is a tool out that does proper UMI quantification! I will retire my [heuristic method](https://github.com/vals/umis) and recommend this in it's place.
There…
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Hi
Thanks for your great tool.
I want to perform ASE calling from 10X scRNA-seq data. Is there an example file for barcodes file(barcodes and their group/cell mapping) so that I can follow the …
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This issue shows that problems of partial loading configuration into scripts. Partial loading requires more variables to be created to separately load configuration into these script
```yaml
# agg…
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Hi,
I am trying to analyze some newly generated scATAC data from Illumina and may have more than 20,000 cells which cellranger-atac count is unable to properly analyze. I would like to use the defaul…
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Hi - thanks for a nice tool! I have a quick question regarding the best approach for using cellsnp/vireo in our experimental setup:
We have generated data from 8 separate 10x Genomics single-cell rea…
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Can this pipeline also demultiplex reads from cell barcodes?