question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
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@tiphainemartin-15107
Last seen 10 months ago

Hi,

for the ones that created the tutorial "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell" https://osca.bioconductor.org/zeisel-mouse-brain-strt-seq.html Could you tell me more about which methods you used to do "After sequencing, expression was quantified by counting the number of unique molecular identifiers (UMIs) mapped to each gene."

We would like to analyze as a set of data from this GEO "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109308", the paper do not explain and share the method used to do the QC, mapping and quantification. So we are thinking to use the method that you used in this tutorial and then use some tools in bioconductor to do other analysis.

Thanks, Tiphaine

STRT-Seq single-cell tutorial • 120 views
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Aaron Lun ★ 26k
@alun
Last seen 17 hours ago
The city by the bay

I just downloaded the counts from GEO, I didn't do any of the remapping myself. That particular sentence just specifies generally that quantification was done, not that I actually did it myself.

So if you want to repeat the quantification from the FASTQ files, I'm afraid I can't provide much specific help here. I would point to scPipe as a package I've used successfully in the past to deal with arbitrary (in particular, non-10X) datasets, especially in cases involving customized cell barcoding schemes.

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thanks for this clarification.

Tiphaine

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