Questions tagged [scrnaseq]

Use this tag for questions related to single-cell RNA-seq.

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14 views

CITEseq different sequencing depth normalization -- Seurat

New technician ruined his first 10X CITEseq experiment on cells counting level and the ratio between replicates is 14k:2.2k:0.8k ncells. How should I now normalize protein data (ADT) from experiment ...
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0answers
18 views

Calculating percent mouse cells per sample

I want to see the correlation between % mouse reads per sample vs % mouse cells per sample. I've already calculated the % mouse reads per sample but I'm stuck on calculating the % of mouse cells per ...
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18 views

A very large number of clones in BCR reportorie

I am using mixcr to convert fq.gz raw data file (single cell BCR sequencing) to txt files with the names such as JX01_d3-B.clonotypes.IGH.txt , Then I use the immunarch to load the file to explore the ...
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1answer
36 views

Problem with Seurat reference mapping

I have 10X scRNA-seq multiome's 3' poly-A capture (scRNA-seq+ATAC-seq) from PBMC Using Seuratreference mapping, I mapped my scRNA-seq part on reference PBMC (for ...
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83 views

Understanding the dot plot from seurat

I am working with single cell data and using seurat to analyze the results. Often in manuscript, we see the dotplots showing the expression of the marker genes or genes of interest across the ...
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1answer
62 views

sctransform - mitochondrial expression filtering / transformation

I have a Seurat object which has a high expression of mitochondrial genes ...
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0answers
68 views

Creating new seurat object with new matrix

I'm trying to do a cross-species comparison between the patient TME vs. the PTX TME to understand gene expression conservation. I have already converted between mouse and human genes giving me a ...
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1answer
44 views

Avoiding the warning 'The following features were omitted as they were not found in the scale.data slot for the SCT assay' in Seurat

I have a Seurat object I want to plot a list of genes but I got a warning saying most of genes removed I have tried with both my genes of interest and all variable genes but the results is very ...
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1answer
29 views

Find corresponding symbol for gene used in Seurat

I have a Seurat object ...
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1answer
62 views

TCR-seq or scRNA-seq

I need idea, intuition, suggestion please I have 10X scRNA-seq of PBMC (multiome's 3' poly-A capture), can I capture ...
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1answer
22 views

Sample versus subject in scRNA-seq

I am reading this paper, where the authors mention We apply SAUCIE to the batch correcting, denoising and clustering of an 11-million cell mass cytometry dataset with 180 samples from 40 subjects in ...
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45 views

Making a box plot of the proportion of cells in each cell types in two groups

I have number of cells in three cell types T, B, M in a Seurat object For two groups of patients, cancers and controls like ...
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31 views

How to interpret scRNA-Seq cell dynamics from scVelo and CytoTrace results

I have the following scRNaseq analysis done with scVelo and CytoTrace. My understanding is as follows: scVelo arrows lead from less differentiated (more stem cell) to more differentiated (e.g. ...
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1answer
85 views

Seurat heatmap for two conditions

I have a Seurat object of four cancers and four controls ...
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2answers
69 views

Help with Seurat QC ambiguity

I have four PBMC samples from 10X scRNA-seq ...
2
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1answer
71 views

SCTransform Warning: in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Running SCTransform on my seurat object produces the warning: Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached What does this warning mean? ...
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2answers
57 views

Merging two dataframes in R

I have a file with cluster number of a scRNA-seq and corresponding annotated cell type like ...
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1answer
39 views

Filtering cells from values in metadata

I metadata slot of Seurat object I have mapping score of each cell to a reference PBMC data like ...
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1answer
39 views

What does this Seurat argument mean

I have extensively read about percent mito in Seurat but I got more and more confused Let's say we want to keep cells with ...
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1answer
53 views

Seurat Dimplot with different clustering IDs

In Seurat metadata I have assigned cells to some cell types with different resolutions I have added the cluster identities to the object via Idents: ...
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3answers
95 views

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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2answers
96 views

10X scRNAseq: Sample mix-up

The student who was working on scRNA seq of KO and WT lines has made a mistake and he mixed both lines and generate the final sequencing data. Now, we are having gene expression data but don't know ...
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1answer
182 views

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 ...
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2answers
154 views

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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1answer
44 views

How to run GSEA analysis on R studio using DEG file list generated from scRNAseq analysis

I want to draw the standard plot of GSEA on Rstudio. I have a data frame that consists of a list of DEGs as below. Actually, I put the DEG list directly to PANTHER that resulted in the GO or pathway ...
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25 views

Is there an easy way to identify nuclear genes using scanpy?

This question has also been asked on Biostars Scanpy has documentation where mitochondrial genes could be easily filtered out using ["MT"]. I was wondering if anybody has information on ...
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2answers
78 views

Removing cells zero for a gene from a scRNA-seq data

I have a big single-cell RNA seq data ...
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0answers
15 views

Clustering by individual tissue population post integration of two datasets

Sorry if this question has been asked. Post batch correction and integration of two datasets, where cells of multiple different tissue types are present, I want to run clustering on cells of ...
2
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1answer
53 views

Pseudotime analysis on multiple samples

I am using Monocle3 to run pseudo time analysis on samples at two different conditions (samples are paired). My question is, is it valid to combine all the cells ...
2
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1answer
44 views

Connection between Detected Genes and The Read Counts

I have been trying to understand the Seurat for analysing scRNA-seq data. It comes to my mind that the main data is organised in the Seurat object with rows as genes and columns as the cells, and the ...
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1answer
76 views

Getting conventional gene symbol for Seurat [duplicate]

I have a Seurat object made by human single cells I am mapping some genes on that but no sign of expression When I GOOGLE for those genes I see the genes have different names How I know Seurat uses ...
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1answer
54 views

how to get normcounts for singlecellexperiment object?

I need to perform differential expression analysis using the scDD package from R, but I am not able to since I miss the normcounts assay in my SCE object (of course in the example they show, the assay ...
3
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2answers
80 views

How do I increase the sensitivity of Salmon Alevin?

I'm in a little bit of a bind with targeted single-cell sequencing. I'm trying to match up our reads to the targeted amplicon panel (418 targets), and all but one have matched successfully with Salmon ...
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0answers
17 views

Average ratio of spliced and unspliced mRNA in human scRNA-seq data

I am currently doing RNA Velocity Analysis using scRNA-seq data from human blood and skin. The RNA Velocity is calculated using the balance of spliced and unspliced mRNA. One thing my PI and me were ...
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1answer
44 views

Why am I getting empty expression data from GEO?

I am trying to analyze the scRNAseq data from this study. In their Method section they write: The accession number for the RNA and DNaseq data reported in this paper is GEO: GSE116237. When I go ...
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1answer
210 views

Error in FindIntegrationAnchors- Seurat package

I am working on integrating a labelled single cell RNA seq cell atlas with an unlabelled one. I am wondering how do I determine the value of max.features when integrating two single cell RNA seq ...
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1answer
46 views

Challenging benchmarks for supervised learning on sparse scRNA-seq data

One challenging aspect of modeling scRNA-seq data is data sparsity, that is, scRNA-seq measurements typically suffer from large fractions of observed zeros (i.e. dropouts), where a given gene in a ...
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1answer
31 views

Is there a difference between any scRNA-seq visualization and pseudotime?

Is there a good definition of pseudotime? Some tools are clearly labeled as pseudotime and produce values along a trajectory, but there are more complex approaches that involve branching and ...
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35 views

Why could I be having only NAs for p_val and p_val_adj in Seurat DGE analysis?

I am doing a differential gene expression analysis to find out genes that are differentially expressed in one cell type from the lung in two conditions, control and idipathic pulmonary fibrosis (IPF). ...
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0answers
38 views

10x Single-cell RNA-Seq - Updating gene symbol with latest ensembl release - Ensembl IDs missing

I am trying to update the gene symbols provided by the 10x human precompiled reference (2020-A), using the mapping Ensembl ID to gene symbol provided in release 102. However, I found out that 56 of ...
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0answers
40 views

Clusters in scRNA of Glioblastoma

There is a scRNA dataset on Glioblastoma from 10xgenomics. Unfortunately, there seems to be no research paper related to that data. Question 0 : May be there is paper ? How to find it ? I am not ...
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60 views

Genes associated with digestion in single cell RNASeq

I am reading Saunders et al. (2018). In the methods' subsection "ICA based analysis and clustering" (independent component analysis), a set of independent components from ICA is labelled as &...
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1answer
135 views

shiny code with seurat object

I am trying to create a shiny board for my scRNA seq data. I have saved my seurat objects adn I use following code as below: ...
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1answer
287 views

Seurat Violin Plot: Why do dots align in one row?

I am analyzing a rather small scRNAseq dataset (39797 features across 3522 samples) and I have observed that dots in the violin plot are plotted in one line next to each other rather than in a cloud ...
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1answer
53 views

Bootstrapping cell type identifications (scRNA-seq)

I have scRNA-seq data held in a SEURAT object, and cell-types were identified with SingleR (essentially a vector of strings - ...
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1answer
89 views

What is the best way to address the question of doublets and multiplets in a single cell RNA seq data set?

I have attached a histogram plot of the number of genes per cell in a single cell RNA seq data set of lung endothelial cells. I do not find a bimodal or multimodal distribution of the number of genes ...
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1answer
564 views

Seurat FindMarkers() output interpretation

I am using FindMarkers() between 2 groups of cells, my results are listed but i'm having hard time in choosing the right markers. Do I choose according to both the p-values or just one of them? If one ...
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1answer
114 views

Differentially expressed genes analysis in Seurat

For the differentially expressed genes analysis, is it possible to check for DEGs based on the levels already identified in the object? For example, my dataset contains cells from 11 subjects, which ...
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1answer
3k views

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'...
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43 views

Alternatives to imputation for single-cell RNA-Seq analysis to increase statistical power of DE analysis

I have a small scRNA-Seq dataset (n = 357, inhibitory neurons). This set of cells is split almost evenly between two conditions (Case and Control). I would like to test for differential expression ...

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