Questions tagged [scrnaseq]
Use this tag for questions related to single-cell RNA-seq.
288
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How to add ATAC data to a Seurat object using the Signac package without starting from an .h5 file?
I am attempting to run a multiomic analysis on some single cell RNA-sequencing data and ATAC-seq data. I have downloaded the scRNA-seq files from GEO in the format of (matrix.mtx.gz, features.tsv.gz, ...
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snRNA-seq analysis: getting NA for certain target genes
I'm doing snRNA-seq analysis of a rare disease. I've gotten upto to finding the markers and getting target genes for a specific protein. However, I'm noticing that a lot of these target genes are ...
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Demultiplex double hashed cells using Seurat (R)
I am using Seurat to demultiplex my single-cell RNA data, which also has HTO data for hashing. Each cell is hashed once based off it's origin ie organ1, and then hashed based off the cell type ie cell ...
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What is the significance of the weak inferCNV signal in non-malignant cells in culture that underwent scRNA-seq?
I'd be grateful for an opinion on the attached infercnv heatmap as InferCNV Github support has been paused. We performed scRNA-seq on human induced pluripotent stem cell (iPSC)-derived brain organoids ...
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Understanding the dot plot from seurat
I am working with single cell data and using seurat to analyze the results. Often in manuscripts, we see the dotplots showing the expression of the marker genes or genes of interest across the ...
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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
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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 ...
CommunityBot
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Most-abundant isoform identification using 10x scRNASeq 5' short-reads
I have read a couple of publications related to the question being asked here, and have concluded that quantification of isoforms for scRNASeq experiments is typically coupled with long-read ...
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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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Find up/downregulated gene lists across scRNA-seq samples
I have two separate scRNA-seq datasets that are different batches. I want to get genelists of up/downregulation of one cluster in one dataset compared to another cluster in the other dataset.
I ...
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MULTI-Seq snRNA-seq results thousands sample barcodes while there should be only 9
I have a dataset resutled from libraries by MULTI-seq and standard 10x Genomics Chromium Single Cell 3’ Reagent Kits v.3. The sample barcode is prepared using HTO approach
When doing demultiplexing, I ...
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Is it possible to integrate a bulk and a pseudobulk (previously scRNA or snRNA seq) dataset
I have recently sequenced a bulk dataset. However one of my conditions has a lot of contamination from other cell types. I was thus thinking of using a publicly available single-cell dataset of my ...
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After changing the idents of cells in seurat, how can I get back to original ident?
I am analysing the scRNA-seq data using Seurat, in the annotation step, I change the idents of cell manually using the function RenameIdents:
...
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Memory issues in scrna_seq pseudobulk aggregation (for muscat Differential State Analysis)
I am new to working with scRNA-seq datasets and I keep running into memory issues when trying to perform differential expression analysis on my data. I know some memory trouble is to be expected with ...
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How to import the average expression matrix for all detected genes in each cluster into Seurat？
I download a matrix which has 19 columns and the first column is gene names, other is cell cluster:
In fact, I just want to plot the feature plot which like this:
My idea is to use the function <...
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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 (...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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-...
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Low custom tdtomato gene content
I have a set of scRNA-seq samples expressing TdTomato, which has high content in microscope. I followed the 10x cellranger pipelines to finsh the work, my procedures are as follows:
added TdTomato on ...
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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 ...
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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 ...
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Featureplot by co-expression of some genes
I want to identify MDSCs cells which don't not express HLA-DRs (HLA-DR negative) but express ...
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How to split a Seurat cluster in several subclusters?
I've analyzed my scRNA-seq data and have a couple of Seurat clusters that show more than one cell type in each cluster. (for example, cluster 9 shows both NK and CD4 cells)
How can I split a cluster ...
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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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Seurat VlnPlot presenting expression of multiple genes in a single cluster
Seurat VlnPlots are most commonly used to visualize differences in any given gene expression across multiple clusters or cell types. For example:
...
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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 ...
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Parsing gene names to detect organism from h5ad input
I have one function that is for reading .h5ad files
...
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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 ...
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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 ...
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Assigning subcluster idents to original object
I have a scRNA-seq Seurat object I've analyzed, and I noticed that for some of the clusters, there's more than one cell type.
I've created a subset which and run FindClusters again to label the cell ...
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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
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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 ...
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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 ...
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h5ad file format filter
I'm trying to do simple filter for single data that is stored in h5ad file format using this
...
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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 ...
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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 ...
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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 ...
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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 ...
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how to filter out cell after doing QC
I was wondering that the threshold that we set after doing QC in Seurat. there is an example
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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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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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Gene names from components in NMF analysis
This question was also asked on Biostars
I am using Rcppml package in R for my NMF analysis, I have a matrix from single-cell analysis. I have cells scores and I wanted to know how to extract genes ...
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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 ...
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