Delaney Sullivan

Just updated the CLI usage :) Will be working on additional documentation.

These are known architecture issues; see https://github.com/pachterlab/kallisto/issues/431 There will be easy options to disable such optimizations in future releases.

@sbresnahan can you post the exact commands you’re running? And can you try the official binaries on the Releases page to make sure it’s not a compilation error? [kallisto_LongKmer_NoOpt-v0.51.1.tar.gz](https://github.com/pachterlab/kallisto/releases/download/v0.51.1/kallisto_LongKmer_NoOpt-v0.51.1.tar.gz)

Very strange — quant-tcc seems to have issues with the input files supplied. If you are able to upload the files somewhere (the files supplied to quant-tcc) and email them...

Oh good catch! And yay!

kallisto version 0.50.0 utilizes an updated kallisto index. Therefore, if you made an index using an older version of kallisto, it will not work with kallisto 0.50.0. As the message...

Yeah, don't worry about the version numbers -- it's just for our own internal use (and those numbers are arbitrary and simply to prevent memory corruption when someone uses a...

Nope, but here are a few suggestions: 1. In your transcriptome reference, you could split up the transcript(s) associated with the gene into two parts: the 5' part and the...

Yes, they are mutually exclusive. We are still in the process of updating genomebam/pseudobam, but it's mostly an auxiliary feature that isn't part of standard kallisto use. genomebam works as...

https://github.com/pachterlab/kallisto/releases/tag/v0.48.0 Most of them were bug fixes and performance improvements.