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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Brcode Rank Plot y-axis scale #227

Closed MartaBenegas closed 1 year ago

MartaBenegas commented 1 year ago

Hi!

Sorry if it's a dumb question, but I don't understand how the y-axis values are calculated in the Barcode Rank Plot. I've only encountered one explanation on this webpage. Here it says that the y-axis is on a logarithmic scale, but I would like to know how is it calculated.

For example, with my dataset I obtained the following result: image

If I calculate different logarithms of the median UMI counts per cell, the numbers are really far from 10k or even 1000, which is what I would expect since I assume that the cells in the final count table should fall in that region:

log10(4957) = 3'695... loge(4957) = 8'5... log2(4957) = 12'275...

Thank you in advance!

evolvedmicrobe commented 1 year ago

The scale is logarithmic in the sense that there is an order of magnitude difference between the tick marks on the axes, e.g. 1/10/100/1000/10K/etc. However, the values displayed are not log transformed, they are just the UMI counts, so the 4957 median value is between the 1K and 10K tick marks.