Dear all,

Is there a way to use swappedDrops on Kallisto output, rather than CellRanger's?

Kind regards, Mike

I don't know much about Kallisto's output format, but if you can manage to extract the relevant pieces of per-molecule information and load them as lists, you can run removeSwappedDrops(). The documentation for the function will describe this in more detail, but the general idea is to create lists of vectors where each vector corresponds to a sample and each element of the vector corresponds to an individual transcript molecule. So you'll have one list of vectors for the gene ID, another list for the read counts, another list for the cell barcodes, and so on.

Probably the trickiest bit is the list for UMIs; each UMI is represented as a 2-bit encoded integer rather than a string. The exact encoding doesn't matter as long as two molecules will only have the same UMI value iff they have the same UMI sequence. Check out ?encodeSequences for more details, but you don't have to follow that specific scheme.