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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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cellranger atac count (force cells issue) #232

Closed samandmac closed 8 months ago

samandmac commented 8 months ago

Hi there,

I've recently run cellranger-atac count, but for some reason in one of the samples it is using --force-cells even though I did not specify to in the code (see below)

cellranger-atac count --id=sample --reference=refdata-cellranger-arc-mm10-2020-A-2.0.0 --fastqs=fastq/sample --sample=sample --localcores=24 --localmem=64

Perhaps a misunderstanding on my part, but why does it automatically use force cells? And will this be affecting my results, because the results for this sample end up with estimated cells of ~20,000 cells.

For reference, none of the samples before or after this particular set have any issues with force cells or similar cell numbers

Thanks for any help offered!

elehnert10x commented 8 months ago

Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.

sbombin commented 5 months ago

Hey @samandmac, I have the same issue, Have you figure out the reason?