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Results tagged with scrnaseq
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user 16676
Use this tag for questions related to single-cell RNA-seq.
3
votes
Is it ok to shortcut cluster annotation in scRNA-seq?
Notably, I am having a hard time differentiating between clusters that I think are macrophages and others that I believe to be B cells.
Generally, that should not be too difficult. Macrophages will …
- 1,511
2
votes
Cellranger count error chnk
I am almost certain that the localmem parameter is the issue here. CellRanger uses STAR aligner under the hood which is resource-hungry. We usually allocate 18 cores and at least 40GB of RAM to CellRa …
- 1,511
1
vote
MULTI-Seq snRNA-seq results thousands sample barcodes while there should be only 9
You don't give much information. However, here is how 10x hashing usually goes:
First, there is the per-cell barcode that tells you which gene expression reads come from one cell. CellRanger and other …
- 1,511
1
vote
Using CSV files continaing scRNA-seq count data from GEO
Please understand that your question is open-ended and essentially you're asking for a complete guidance through your analysis which is not feasible. I recommend to go through either the Seurat tutori …
- 1,511
2
votes
How to identify a low proportion cell subpopulation in the single-cell RNA-seq data?
Run the usual steps including clustering and visualization via something like UMAP and then color the UMAP by these four markers. That assumes that the surface marker separation you see in flow holds …
- 1,511
1
vote
Is it possible to integrate a bulk and a pseudobulk (previously scRNA or snRNA seq) dataset
No, you cannot. It is a basic principle of any experiment that you cannot add data from completely unrelated other experiments and expect any meaningful quantitative readout. There is a batch effect b …
- 1,511