Question: How can I calculate TPM or FPKM units instead of counts?
Answer: Cell Ranger uses unique molecular identifier (UMI) counts for measuring gene expression levels and not read counts. Therefore all secondary analysis steps are performed based on UMI counts. Please see the "Secondary Analysis" section of the Algorithms Overview page for more information.
With the 10x workflow, transcripts are tagged with a 10 bp sequence serving as a Unique Molecular Identifier (UMI). These UMIs enable accurate quantitation of gene expression levels because we can tell when reads are generated from the same mRNA molecule: Assay Scheme and Configuration of Chromium Single Cell 3' v2 Libraries.
In traditional RNA-seq data, complete transcripts are fragmented followed by cDNA synthesis, end repair, and adapter ligation. In this workflow, the probability of sampling a fragment from a long transcript is higher than from a short one. Therefore, it makes sense to normalize read counts by transcript length (e.g. TPM, RPKM, FPKM). However, in 10x single cell 3' or 5' gene expression assay, this gene-length bias does not exist. Therefore, we do not advise on normalizing UMI counts by gene length.