Questions tagged [scrnaseq]

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

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Is it ok to shortcut cluster annotation in scRNA-seq?

I hope you all are doing well. I am currently conducting a scRNA-seq analysis on a data set containing mono-nuclear, non-myofiber muscle and muscle resident cells post injury. My research question is ...
danielpintard's user avatar
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0 answers
9 views

Done miRNA sequencing from animal tissue & have 1 control sample in duplicates 1 treatment group as test. In PCA plot clustering is not there

I have done miRNA sequencing from animal tissue and have control sample in duplicates . Like wise one treatment group as test. In PCA plot clustering is not there. There is very randomness. Is it ...
M Javed's user avatar
2 votes
1 answer
28 views

How to import data from cell ranger to R (Seurat) using Read10X?

I am loading cellranger data into seuratobject as following, but it keeps showing Error in Barcode file missing. Expecting barcodes.tsv.gz the running code and ...
Kent Yang's user avatar
1 vote
0 answers
39 views

Comparing sc-seq combination and bulk-sequencing

I have expression matrices for different cell types, representing the expression of individual cells of that type. They were learned through a generative model, so I am confident they represent the ...
谢润达's user avatar
2 votes
2 answers
30 views

How to perform meaningful Gene set erichment analysis or otherwise find broader themes/functions in different cell populations?

(For context: I'm somewhat new to bioinformatic analyses but am mostly comfortable with R) I have identified transcriptomically and morphologically different cancer cell populations within a patient (...
immunoLogical's user avatar
1 vote
0 answers
24 views

Why my FeatureScatter looks so different, and what does that mean?

I' am doing a sc-Seq analysis on a dataset from 10x genomics, using Seurat. I followed the standard workflow and I also did it with the SCTransform workflow. The results are very different when I plot ...
Rodrigo Angel Hermoza Sanchez's user avatar
1 vote
2 answers
34 views

Can anyone share insights or provide the complete mRNA sequence for tdtomato-WPRE for scRNA seq analysis?

I'm currently immersed in research involving the Rosa26-tdtomato (Ai9) mouse line. We performed scRNA seq and analysis focusing on tdtomato-expressing cells but faced a challenge with a lower-than-...
Outlander's user avatar
0 votes
1 answer
53 views

What is a common number of cells per cell type in single cell RNA Seq?

Good afternoon, I just started working with Single cell RNA Seq and I am trying to understand what is an average / possible number of cells per sample. I am looking at a dataset of 7 patients with ...
Bine's user avatar
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0 answers
25 views

Suggestion for way foward with upregulated genes

I am working with single cell RNA data- control and treated. I analyzed and got a list of upregulated genes. Upon doing pathway analysis all the genes were of apoptotic pathway. But these genes can ...
subhiksha sundaram's user avatar
-1 votes
1 answer
93 views

Single Cell RNASeq Knee Plot - Collapsed vs Non-collapsed Reads

I am trying to adapt combinatorial index reads with some modifications for long read sequencing; it's a custom approach, not a commercial kit. I have a question about using Knee Plot for identifying ...
user3377241's user avatar
1 vote
0 answers
39 views

Parsing gene names to detect organism from h5ad input

I have one function that is for reading .h5ad files ...
kcm's user avatar
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-1 votes
1 answer
170 views

Using CSV files continaing scRNA-seq count data from GEO [closed]

I'm completely new to scRNA-seq analysis (and to most of Bioinformatics as well) so I apologize if this was asked a million times before. I am trying to get the single cell expression data of lymph ...
Newbie Bioinformatician's user avatar
0 votes
1 answer
113 views

is it possible to count cell in Violin plot in seurat?

I tried to quantify the number of cells of Fzd9+ Macrophage. how can I know the cell count? thank you
kiseoking's user avatar
0 votes
1 answer
23 views

Looking for datasets of RNA-Seq (or scRNA-Seq) for L1 larvae C. elegans

I was wondering if anyone know of a repository for C. elegans data sets, specifically in L1 larvae stage. Are there any papers or GEO-sets for this organism at this stage? thanks Assa
Assa Yeroslaviz's user avatar
0 votes
3 answers
291 views

How to handle technical replicates in cellranger count?

I'm working with cellranger count to annotate some publicly available fastq files (SRX7888073). For each sample, 4 runs are available, which I assume represent technical replicates. How do you ...
David's user avatar
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2 votes
1 answer
125 views

Mapping single cell data with annotation

Entry level Bioinformatician here. I am trying to map my single cell data with standard annotation file or assign my Seurat cluster to cell types. I have used the singleR and celldex package to map it ...
Apple Ball's user avatar
-1 votes
1 answer
99 views

Gviz Coverage Plots

This question has also been asked on Biostars I have two bam files from single-cell RNA sequencing mapped to the reference genome using CellRanger, I can view them in IGV and I have a particular ...
A4747's user avatar
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1 vote
2 answers
263 views

h5ad file format filter

I'm trying to do simple filter for single data that is stored in h5ad file format using this ...
PesKchan's user avatar
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1 vote
1 answer
479 views

Low fraction reads in cell metric in snRNA-seq data

For some of our snRNA-seq samples we are finding low fraction of reads detected in single-nuclei rna-seq samples from cellranger, while the other metrics are perfect. While I understand this could be ...
Hirak Sarkar's user avatar
1 vote
0 answers
105 views

Correlate ssGSEA score with Seurat's scaled expression data

I want to check the correlation between the expression of a given "test_gene"* in each cluster within a scRNA-seq database with the expression of a signature (i.e., gene sets whose ...
samge's user avatar
  • 11
2 votes
3 answers
2k views

Merging multiple seurat datalist together

I have a R script that subsets out the tumor cells from 6 different individual seurat objects. It gets a list of file paths for all RDS files containing the expression data for multiple datasets in a ...
mmpp's user avatar
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0 votes
0 answers
45 views

How to remove orig ident. already data normalized, scaled assigned cluster/

How to remove orig ident. already data normalized, scaled assigned cluster/ Example, I have 4 sample data. like 1-control, 2- treatment with A, 3- treatment with B, and 4- treatment with C, I want to ...
Sandi's user avatar
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1 vote
1 answer
261 views

Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)

I can't seem to find a clear answer to this question, so here it goes: I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody ...
h3ab74's user avatar
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1 vote
1 answer
74 views

In cellranger, can I change the minimum number of reads for autodetecting chemistry?

I ran cellranger multi on a TotalSeq B dataset and got this error ...
Sam's user avatar
  • 11
1 vote
1 answer
414 views

Determine expression values for a defined list of genes across different clusters in scRNA data using seurat

I am analyzing publically available scRNA seq datasets on R using Seurat. I have created a seurat object, clustered and annotated different cell types. Now, I am interested in comparing the expression ...
Ahmed M.'s user avatar
1 vote
0 answers
451 views

How to plot average gene expression in scanpy?

I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it. I did ...
pythonbeginner's user avatar
1 vote
2 answers
612 views

How to calculate cell type percentage in every sample

I have a Seurat object (metadata) with the single R samples consisting of cell types and sample types columns. I am trying to make a table that has a sample and percentage of cell types for each ...
Yogesh Budhathoki's user avatar
2 votes
0 answers
187 views

How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy?

I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it. I did ...
pythonbeginner's user avatar
1 vote
1 answer
286 views

Cells with zero expression of a given gene

I have scRNA-seq from PBMC analyzed by Seurat. I am seeing for most of genes a lot of cells have a zero expression like this gene So 268 single cells have the expression level == 0 And I am more ...
Zizogolu's user avatar
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1 vote
1 answer
361 views

How do cellranger and cellbender call cells? What is the difference between them?

When I use cellranger or cellbender to filter cell from raw RNA count matrix, the results they output are allways different. Each of then can call some cells not appearing in other's result. SO, how ...
Cheng Lyu's user avatar
2 votes
0 answers
33 views

Creating meta cells from scRNA-seq and scATAC-seq for GRN analysis

We have two 10X Genomics scRNA-seq and scATAC-seq datasets generated from similar cells, but in different experiments - separately, not using the multiome platform. Now, we are trying to use Pando (...
iYassin's user avatar
  • 121
2 votes
1 answer
56 views

How to identify a low proportion cell subpopulation in the single-cell RNA-seq data?

The cell subpopulation that I am interested in only accounts for around 1.2% of the total cells. I have previous FACS experiments that sort out the subpopulation from the samples (using markers CD166+ ...
Wang Ming's user avatar
  • 101
2 votes
0 answers
125 views

pyScenic CLI for ctx is giving error: Not a single module loaded

Hi I ran pyScenic's ctx via the command in command prompt: ...
Yihua's user avatar
  • 21
2 votes
1 answer
65 views

Examples of machine learning approaches to validate results where ground truth is lacking?

I am currently looking into some of the published methods for deconvolution of spatial transcriptomics data where each spot does not have single-cell resolution. These methods all rely on cell type ...
Alos's user avatar
  • 21
2 votes
1 answer
851 views

How to change the position of groups colors in DimPlot of Seurat

I have a Seurat object and plotted the Dimplot for UMAP visualization for 2 variables, as shown in the image below. Now, the problem is that I want the group by variables such as ...
cst's user avatar
  • 123
1 vote
1 answer
143 views

umap failed to cluster the cells

I tried umap visualization with scanpy : ...
Dan Li's user avatar
  • 141
0 votes
1 answer
40 views

Keep first 20 nucleotides of sequences using R

I have an Excel sheet from the CRISPR library where I have sequences of gRNAs (with 30 nucleotides) in a column and I only need to keep the first 20 nucleotides for those gRNAs and delete the rest ...
user16558's user avatar
0 votes
1 answer
18 views

Understanding regularization step in Meta-cell pre processing

I'm reading through this paper: Baran, Y., Bercovich, A., Sebe-Pedros, A., Lubling, Y., Giladi, A., Chomsky, E., ... & Tanay, A. (2019). MetaCell: analysis of single-cell RNA-seq data using K-nn ...
Angus Campbell's user avatar
1 vote
2 answers
330 views

Error in dimnamesGets(x, value) when trying to read data using Seurat package

This question has also been asked on Biostars I am trying to create a Seurat object using the package "Seurat". When I am reading my raw files using the function ...
Gen's user avatar
  • 21
5 votes
3 answers
119 views

Ubiquitous regulation of highly specific marker genes

I am fairly new to scRNAseq analysis and keep running into the same problem in the two datasets I am currently working with. We work with kidney inflammation and have two new mouse models, which we ...
Smeerlap's user avatar
0 votes
1 answer
295 views

Correct way of merging scRNAseq datasets of healthy and tumor cell?

While merging datasets from similar biological conditions, but different experimental conditions is a well-studied topic, and there are many batch correction techniques available. What I want to ...
Divyanshu Srivastava's user avatar
0 votes
0 answers
438 views

extracting raw gene counts based on the cluster generated by seurat

I'm new to single cell sequencing analysis. I have made different clusters using seurat. Now I would like to extract the raw gene counts based on the cluster generated by seurat. i have provided my R ...
Manojkumar K's user avatar
2 votes
0 answers
105 views

I am trying to use slingshot for pseudotime analysis. I am getting error while saving an object as dataframe

When I run following code, I get error at - slingshot_df <- data.frame(colData(sce)) the error is : Error in as.vector(x) : no method for coercing this S4 ...
Snehal Nirgude's user avatar
2 votes
0 answers
23 views

Avoiding false anticorrelations between individual genes per cell in single-cell RNAseq

When analysing a single-cell RNAseq dataset, one question I like to ask is: At a single-cell level, are these two genes correlated (expressed together) or anticorrelated (only one or the other is ...
D Greenwood's user avatar
2 votes
1 answer
457 views

Are the doublets in the tutorial dataset in Scanpy/ Seurat already filtered?

I noticed the tutorials that Scanpy and Seurat use do not demonstrate doublet removal in their down stream analysis. Is the dataset output of cellranger count already doublet removed or do I need to ...
Emily Nwo's user avatar
1 vote
1 answer
856 views

Cellranger results have too many cells

I have the results of cellranger analysis for single-nucleus RNA seq data that was done by someone else. So I do not know which parameters were used for cellranger. In the results, there are 77000 ...
Yulia Kentieva's user avatar
1 vote
3 answers
3k views

Bar Graph of Expression Data from Seurat Object

I am looking for a way to present some single-cell RNA sequencing data on expression of a certain gene. My dataset has 2 variables, cell type and condition. I'm looking to create a grouped aligned ...
Anonymous K's user avatar
1 vote
1 answer
181 views

Aligning scRNA-seq fastq to .bam without cell barcodes

I would like to convert the fastq files from this dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98679 to .bam files. The group did not provide the scripts they used to to their ...
Angus Campbell's user avatar
2 votes
0 answers
34 views

Is it possible to cluster a sc-RNAseq expression matrix with weighting or embedding?

I have an RNAseq mouse retina gene expression matrix(24659,49300) to cluster effectively. Here is a sample(7,4): ...
nomad culture's user avatar
2 votes
1 answer
639 views

how to calculate the expression values per gene for all cells

I'm currently working with a seurat object and I'd like to calculate the expression values per gene for all cells within a particular cluster. I've gone ahead and subsetted the cluster of interest. <...
mmpp's user avatar
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