Questions tagged [scrnaseq]
Use this tag for questions related to single-cell RNA-seq.
20
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Inspection of gene expression in scRNA-seq data
I am running the data preprocessing pipeline for scRNA-seq data presented here.
3.8.6.1 Gene expression
In addition to removing cells with poor quality, it is usually a good idea to exclude genes ...
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determining doublets in single-cell RNA-seq
Doublets are a known problem with scRNA-seq experiments, where 2 or more cells are sometimes captured instead. To determine their presence, there are studies that mix multiple species (such as human ...
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What are doublets in single cell RNA-seq data?
I am reading The Tabula Muris Consortium et al. (pp).
In some organs, cells with more than 2 million reads were also excluded as a conservative measure to avoid doublets.
How exactly is a “doublet”...
- 1,813
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Drawbacks of upper quartile normalization for scRNA-seq data
I would like to use Upper Quartile normalization for scRNA-seq data defined as:
The upperquartile (UQ) was proposed by (Bullard et al. 2010). Here each column is divided by the 75% quantile of the ...
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Order of batch effects removal, data imputation and library size normalization in scRNA-seq data
I am preprocessing scRNA-seq data. What is the best practice in use to run both ComBat for batch effects removal, data imputation (to mitigate dropout) and library size normalization?
I thought that ...
- 1,813
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3
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Improve scRNA-seq dataset for further analysis
I got a dataset from C.Elegans scRNA-seq paper:
GSM2599701_Gene.count.matrix.celegans.cell.Rdata in ...
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2
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Detect transcript isoform abundance for a specific gene in scRNA-seq
I want to detect the count of isoform transcripts for a specific gene in scRNA-seq data. Data is coming from cells of Mus Musculus.
For transcript isoforms I mean the different alternatives provided ...
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5
votes
2
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Assign cell types to groups of cells based on their gene expression profiles
I have large filtered, normalized dataset of scRNA-seq data of C.Elegans species. Rows are genes (10 000), columns are cells (66 ...
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1
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No counts for added gene in cellranger (scRNA-seq)
I have a set of scRNA-seq samples enriched with FACS for cells expressing a specific gene reporter (TdTomato). In particular the gene I want to report has positive counts in the resulting matrix for ...
- 1,813
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3
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The confusion of using TPM (transcripts per million)
It is shown that TPM values are not suitable for DEG analysis but good for within-sample comparison since TPM normalized the gene length. My question is first: if TPM is not suitable for across ...
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RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'
I am trying to run UMAP in the following way:
...
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3
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1
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How to set the position of groups in a Seurat object on a FeatureHeatmap plot
I am analysing singe cell sequence data and I have followed this tutorial, https://satijalab.org/seurat/pbmc3k_tutorial.html to perform QC and various differential analyses using the Seurat package on ...
- 547
2
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color by clusters and sampled in Seurat
I have a Seurat object
I want to have both cluster numbers and coloured cells by sample names like this figure (from a Nature paper)
I have tried group.by argument ...
- 2,232
2
votes
1
answer
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Changing active.ident in Seurat
Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...
2
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3
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How to detect mismatch before mapping in RNA-Seq data
In the methods of this paper, the authors say:
Reads were then filtered based on quality score in the UMI region. Any read with >1 low-quality base (phred <=10) were discarded. Reads with more ...
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2
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Adding metadata to Seurat object
I have a Seurat object of 8 patients. I want to add metadata to that so that I have origin of each cell. At the moment UMAP just shows a bunch of cells while I want to color clusters by sample
This is ...
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How to filter ribosomal RNA from scRNA-seq data
I want to filter out ribosomal RNA from scRNA-seq data (downloaded from here). Is there a list of known ribosomal RNA?
The only solution I found is SortMeRNA, however it works with raw sequencing ...
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0
votes
1
answer
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sctransform - mitochondrial expression filtering / transformation
I have a Seurat object which has a high expression of mitochondrial genes
...
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3
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isSpike function in SingleCellExperiment package is deprecated?
I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use isSpike function to filter out ERCC (control) and MT (mitochondrial RNA) reads, ...
