Question: What is the recommended sequencing depth for Cell Ranger DNA in non-human experiments?
Cell Ranger DNA was developed using human cells, however you can run non-human cells if you create a custom reference (https://support.10xgenomics.com/single-cell-dna/software/pipelines/latest/advanced/references). This should be considered experimental.
The sequencing depth recommendation for human is 750,000 read pairs per cell (https://support.10xgenomics.com/single-cell-dna/sequencing/doc/specifications-sequencing-requirements-for-single-cell-dna), which is approximately 350-400 usable reads per Mb (https://support.10xgenomics.com/single-cell-dna/software/pipelines/latest/interpret/read_depth) for the 3.2 Gb human genome.
It is the usable reads per Mb that determines the sensitivity (and therefore resolution) of the assay. Therefore, the number of read pairs to sequence should be scaled according to the size of the custom genome, with the goal of keeping the final reads per Mb in the 350-400 range. As a simple example, if the custom genome is 6.4 Gb in size, you would need to sequence 1,500,000 read pairs per cell (3 M individual reads per cell).
Note this will be approximate, since the final yield of usable reads may vary depending on the genome.