Entering edit mode
8 weeks ago
firestar ★ 1.5k
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.
Thanks! That works! Slightly more detailed tutorial at Analysis of Smart-Seq3 data with kallisto-bustools.