Questions tagged [scrnaseq]
Use this tag for questions related to single-cell RNA-seq.
265
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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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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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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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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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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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103
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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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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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196
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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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317
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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 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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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 ...
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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
...
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298
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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 ...
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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 ...
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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 ...
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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 ...
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206
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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 ...
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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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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 (...
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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+ ...
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pyScenic CLI for ctx is giving error: Not a single module loaded
Hi I ran pyScenic's ctx via the command in command prompt:
...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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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 ...
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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):
...
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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.
<...
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Single-cell RNA sequencing proper abbreviation [closed]
I wonder which form of a single-cell RNA sequencing abbreviation is correct:
scRNA-seq
scRNA-Seq
In the same single-cell sequencing Wikipedia article, both forms appear.
There is also inconsistency ...
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Different colors in UMAP
I have integrated top ten TCR clones into Seurat object something like below
You are seeing some clones are expressed in more than one cells
So in Seurat I have something like
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Does the number of RNA reads per cell obtained from the 10X scRNA experiment depend on amount of mRNA in given cell?
As we know, the amount of RNA reads per cell obtained from 10X scRNA experiment vary between cells. I wonder if this is effect of technical issues or does the number of RNA reads per cell obtained ...
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How to manage memory contraints when analyzing a large number of gene count matrices? I keep running out of RAM with my current pipeline
I have several hundred scRNA-seq count matrices, each from a different sample. For my other dataset containg a few dozen samples, I simply merged everything together into one Seurat object, but that ...
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scRNA-Seq pseudobulk for marker detection
A standard approach for scRNA-Seq is to partition the single cells into individual clusters, then use a Wilcoxon test to find markers that characterize each cluster (or other statistical methods that ...
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Subsetting out prefix from genes and merging
I'm working with PTX samples (human and mouse), they're aligned to both transcriptomes and so gene names contain hg38- and mm10- at the beginning of each gene. I have eliminated teh prefixes because I ...
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Normalization methods to combine scRNA-seq experiments with different sequencing depths
I am training a classifier to identify a cell type in a particular state of activity using scRNA-seq. There is a large variation in the sequencing depth (reads average per cell) of the testing data (...
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390
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How will Seurat handle pre-normalized and pre-scaled data?
I want to use data from the following dataset:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84371
The data has been TPM normalized, which is not ideal for clustering but I have to work with ...
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415
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Why is bulk RNA sequencing reflecting AVERAGE expression but not TOTAL expression of all cells?
When I am reading papers that compares bulk RNA sequencing and single-cell RNA sequencing, we often see papers describe bulk RNA seq measures the average cell expression.
For example, in this paper ...
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Plotting a gene in Seurat
I saw in the extensive Seurat documentation for Dimplot (dimensional reduction plot), here, you can plot a gene by specifying it with group.by = "gene" but this does not work in practice.
<...
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