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Hi,
I am testing this package with my VDJ data but I found that our output were from Cellranger 5.0, where it miss some columns (see https://github.com/scverse/scirpy/issues/279)
I get errors l…
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Hi,
bc.export.X_to_mtx() output the previous mtx generated by cellranger 2:
barcodes.tsv genes.tsv matrix.mtx
The latest cellranger generated distinct outputs now:
barcodes.tsv.gz features.t…
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Hi All,
I am running velocyto.py to process the 10x PBMCs data (v3.0.0).
My code is 'velocyto run10x -m cellranger-3.0.0/reference/expressed_repeats_annotation/hg38_rmsk.gtf cellranger-3.0.0/sa…
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Hello!
When I use scTE, I have some questions about the number of cells of the results.
I ran cellranger as the code below:
`cellranger count --id ${sample} --sample ${sample} --transcriptome ~…
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I have 3' scRNAseq data from 10X genomics. I ran the data through cellranger so, I have the possorted bam ouput file. I tried to run regtools on the bam file but, the bed output file has ? in the stra…
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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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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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### 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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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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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…