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pachterlab / kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
https://www.kallistobus.tools/
BSD 2-Clause "Simplified" License
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fixed RNA profiling #215

Closed yfarjoun closed 9 months ago

yfarjoun commented 10 months ago

Describe the issue Fixed RNA profiling is a relatively new assay provided by the Chromium system . CellRanger also provides a pipeline for analyzing the resulting data.

I was wondering if the kb team has any best-practices or suggestions for how to run KB on fixed RNA profiling data.

Left to my own devices, I was considering creating a reference from the probes in the probe-set and then running as normal, but I'm not sure if that's the correct approach.

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Yenaled commented 9 months ago

I think this can use the following workflow described here:

https://www.biorxiv.org/content/biorxiv/early/2022/10/10/2022.10.09.511501.full.pdf