Hi,

I have used swappedDrops function to remove potential index hopping UMIs from 10x genomics single-cell data. Recently, we sequenced +100K single cells. When I was processing the data, I found that swappedDrops crashed. I am wondering if there is a limitation to the number of cells swappedDrops can handle. Your inputs/insights will be much appreciated. Thank you.

Best, Joon

As Jonny said, more information is necessary to provide meaningful advice. In the absence of such information, I'll just throw out a couple of scenarios for you to ponder.

• You ran out of memory and your cluster killed the job. Solution: allocate more memory. Expect swappedDrops to use up about 5 GB of RAM per sample (I don't remember the exact numbers).
• You have more than .Machine$integer.max molecules in one of your files. Solution: switch to DropletUtils 1.3.* or higher, which avoids this limitation (up until 2^64 molecules, at least).
• You get a segfault due to a stack overflow. Solution: increase the size of your stack, as discussed here.
• Something else happened, in which case you should show the commands you used, the error message, sessionInfo(), etc. A reproducible example would be great but I doubt you will be able to provide it.

Jonny and Aaron,

Thank you. I will rerun swappedDrops following your suggestions. If I fail, I will get back to you with error messages.

In this analysis, we sequenced ~40 10x GEM samples (~100K cells in total) three times by using NovaSeq. We included all samples in each run.

Joon