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pachterlab / kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data
https://kallistobus.tools/
MIT License
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Required files for technology = smartseq2 #38

Open ostkampp opened 2 years ago

ostkampp commented 2 years ago

Hi,

I tried using kb-python to get raw count matrices from fastq files obtained from smartseq2. I got paired end data and have two fastq files. However, I got an error telling me I need four files. So what exactly does kb-python count expect when using technology smartseq2?

Best

Yenaled commented 2 years ago

Can you show us the exact command you're running and the error message?

DarioS commented 1 year ago

Would not a different toolkit be better-suited for Smart-seq2 data, since it sequences along the entire gene length?

Yenaled commented 1 year ago

No, kallisto is fine for that purpose (and was actually initially designed for full gene lengths)