Tools/pipeline for analysis of smart-seq3 data

Question

[firestar]

I have Smart-Seq3 data and zUMIs refuses to work. Is there any other alternative? Nf-core pipelines rnaseq and scrnaseq doesn't support sm3 yet.

I am also prepared to go down the manual route. Has anyone tried umi_tools or alevin at least to demultiplex the fastqs? Does anyone know if Takara smart-seq-de3 tool handles sm3 data? The example shows that it takes only 2 fastqs as input.

Any tools, examples or suggestions are appreciated.

Answer 1

[dsull]

kallisto | bustools works for smart-seq3

Install it via:

pip install kb-python

Use kb ref to create a reference and use kb count -x smart-seq3 to quantify your smart-seq3 data.

[firestar]

Thanks! That works! Slightly more detailed tutorial at Analysis of Smart-Seq3 data with kallisto-bustools.