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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Rerun `cellranger multi` with different parameters without having to rerun the full alignment ? #140

Closed plijnzaad closed 2 years ago

plijnzaad commented 2 years ago

In a recent cellplex run of ours, the default min-assignment-confidence parameter of 0.9 was too stringent. I have been in contact with technical support about this but apparently you really have to do a full cellranger multi rerun when choosing a different parameter; it can't be done with (e.g.) cellranger reanalyze. It would be very helpful if this were possible, avoiding the alignment steps, saving much time (and diskspace) and allowing easier exploration of the data. Support know about this, but I had forgotten about this github repo so I thought I'd enter it here too, also to see if other users would benefit from this.

evolvedmicrobe commented 2 years ago

Thanks for this feedback @plijnzaad! We're having internal conversations about this, and may have future improvements addressing this.