Delaney Sullivan

OK, yes, rna velocity is just slow with kallisto. This will change in our forthcoming release of kb-python (version 0.28; currently on devel branch), which will be released in the...

Currently, kb count only does transcript quantification for bulk/smart-seq data (where each sample or cell is in a separate FASTA file). For 10X type data, kb count stops at the...

Oh, with such a large matrix, it's computationally intractable. You will definitely need to filter cells. The EM algorithm (which gives you transcript counts) in quant-tcc only takes a few...

No, kallisto is fine for that purpose (and was actually initially designed for full gene lengths)

1. What version are you running? 2. What are you generating a loom file for? 3. As mentioned in multiple other GitHub issues, Signals.SIGILL: 4 typically means you have to...

Sounds good -- install kallisto from source, and also, upgrade kb-python to the latest version (0.28.2).