Option for outputting pseudoalignments to bam not available in kb 0.29.1?

[terencewtli]

Hi,

I am interested in applying standard genetic demultiplexing methods to the pseudoalignments from kallisto. I saw in an earlier issue that the --genomebam option was added? #184

But I don't see it available in the command line options. Sorry if I misunderstood the installation...

version: kb_python 0.29.1
output of kb count --help:
kb_count.log

Installation:

conda create -n kb python==3.10
conda activate kb
pip install git+https://github.com/pachterlab/kb_python

[Yenaled]

genomebam is not available in kb-python — we had trouble integrating it into the newer versions of kallisto so we didn’t release it. We have done some work on adding it back then, so hopefully it’ll return soon.

For demultiplexing, probably best to do it at the FASTQ level.

[terencewtli]

Got it - thanks!