Questions tagged [scrnaseq]

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

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2
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0answers
17 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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0answers
61 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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3answers
675 views

How to import data from cell ranger to R (Seurat)?

I will have some scRNA-seq data. The goal of the experiment will be to see if there is any difference in gene expression between treatment groups using the package Seurat from R. I have read a ...
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2answers
2k views

Percentage of each cluster in Seurat

I am using Seurat to analyze my single cell data. I have 2 conditions, treated and untreated. I am trying to create a stacked bar graph in order to show the differences in cell types for each ...
1
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1answer
140 views

What column and row naming requirements exist with Seurat (context: when loading SPLiT-Seq data)

I'm trying to use Seurat for the first time and am learning about single-cell analysis for the first time, and I'm doing so with split-seq data. (Full disclosure: I'm also a lightweight when it comes ...
-1
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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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0answers
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 ...
1
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1answer
111 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 ...
0
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1answer
578 views

Cell Ranger) Error during performing a test run

I am interested in the analysis of single-cell RNA-sequencing data. I installed Cell Ranger according to the instruction (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/...
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2answers
93 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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0answers
59 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 ...
-1
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1answer
58 views

sctransform - mitochondrial expression filtering / transformation

I have a Seurat object which has a high expression of mitochondrial genes ...
0
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2answers
126 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 ...
0
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1answer
40 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 ...
0
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1answer
28 views

Find corresponding symbol for gene used in Seurat

I have a Seurat object ...
1
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1answer
43 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 ...
0
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1answer
61 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 ...
0
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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 ...
-1
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1answer
80 views

Seurat heatmap for two conditions

I have a Seurat object of four cancers and four controls ...
0
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0answers
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 ...
1
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0answers
30 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. ...
0
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2answers
69 views

Help with Seurat QC ambiguity

I have four PBMC samples from 10X scRNA-seq ...
1
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1answer
153 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 ...
2
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1answer
62 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? ...
0
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2answers
56 views

Merging two dataframes in R

I have a file with cluster number of a scRNA-seq and corresponding annotated cell type like ...
-1
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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 ...
0
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1answer
46 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: ...
0
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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 ...
0
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3answers
91 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 ...
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 ...
0
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0answers
24 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 ...
4
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2answers
170 views

High percentage of poly A sequences in 10X chromium R2 read

I'm currently analyzing two samples of eosinophil cells isolated from mouse lung and the samples are of very different quality. According to the Cell Ranger summary 56% of the reads can be mapped to ...
1
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1answer
494 views

Low Fraction of usable antibody reads in CiteSeq

we performed a combined gene expression and CiteSeq experiment with the 10x VDJ kit and 20 conjugated antibodies and sequenced on hiseq. I used cellranger to process the sequencing output. The ...
2
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1answer
51 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 ...
1
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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 ...
1
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1answer
49 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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1answer
73 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 ...
3
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2answers
145 views

Hemoglobin subunits genes in scRNA-seq

In one scRNA-seq sample I encountered the genes: Hbb-bs, Hba-a1 and Hba-a2. These genes appear on top of the list of the highest expressed genes but the 75% percentile of cells have very low counts. ...
3
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2answers
68 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 ...
1
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0answers
266 views

How to create a legend in FeaturePlot with do.hover at the same time?

you can see in my feature plot I can only see the cells from which sample but I cannot see the legend. And if I change the command I can see the legend but cannot see the sample identities....
0
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0answers
16 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 ...
1
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1answer
88 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 ...
6
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2answers
220 views

How I can test my hypothesises computationally

I have single cell RNA-seq data on about 2000 cells in 9 time point. I have clustered my cells in each time point by Seurat. I am seeing in some time points I have 3 clusters while in another time ...
0
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1answer
201 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 ...
2
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2answers
2k views

How do I add a colour annotation bar to the heatmap generated by DoHeatmap function of Seurat v2?

I am using Seurat v2 for professional reasons (I am aware of the availablity of Seurat v3). I am clustering and analysing single cell RNA seq data. How do I add a coloured annotation bar to the ...
6
votes
1answer
164 views

Aggregate sequencing/mapping/etc. metrics from cellranger across Illumina samples

I have a number of single-cell projects processed with cellranger from 10x Genomics. The pipeline produces a number of handy metrics that are summarized for each Illumina sample in web page. These ...
0
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1answer
43 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 ...
12
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1answer
189 views

scRNA-seq multi-dataset integration for small datasets

There have been a few methods proposed for integration (or batch correction) of scRNA-seq datasets, such as Seurat CCA, MNN Correct, Scanorama, and Harmony. The concern is generally about the maximum ...
1
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1answer
45 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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