Delaney Sullivan
Delaney Sullivan
h5ad is shorter to generate. You need to add mature+ambiguous together (to make “spliced”), and the nascent is the “unspliced”, to do what cellranger does. See the tutorial on that....
--report is a bug, mature+ambiguous manual processing is equivalent to --sum=cell (and likewise for --sum nucleus being nascent+ambiguous), for --cellranger no.
You'll have to filter the cells for the ones that have sufficient total UMI counts. Then the results should be similar.
You can either inspect the knee plot and look for the inflection point or you can try running kb-python with --filter=bustools
The index data structure was completely rewritten (by me and a few others) making it more compact.
The bias option is no longer supported
It's no longer displayed in the command-line help menu. However, the old bias implementation is still kept in the codebase just in case we want to re-support it in the...
Apologies; the kallisto codebase has gotten quite large and it’s difficult to catch and fix various issues that would make it easier for the user. There’s already a lengthy todo...
Library preps have improved and I haven't tested how prevalent such biases remain in more recent datasets. In any case, that option is not used by the majority of users...
I don’t understand the question. Kallisto (by virtue of it being an pseudoalignment algorithm) always retains multimapping information and uses it to generate the estimated counts in the abundance output...