Questions tagged [10x-genomics]
The 10x-genomics tag has no usage guidance.
44
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Error in colSums(cts[[i]]) : 'x' must be an array of at least two dimensions
I'm getting an error when creating the counts from a single cell experiment.I'm identifying shared barcodes as well as lowUMI barcodes with the follow code:
...
-1
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1answer
45 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 ...
-1
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1answer
104 views
sctransform - mitochondrial expression filtering / transformation
I have a Seurat object which has a high expression of mitochondrial genes
...
0
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1answer
89 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
63 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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0answers
47 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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1answer
126 views
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2answers
88 views
0
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2answers
63 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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-1
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1answer
75 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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0
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1answer
41 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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1answer
162 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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2answers
99 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 ...
1
vote
1answer
333 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 ...
0
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2answers
349 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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2answers
83 views
-3
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1answer
108 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 ...
0
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2answers
172 views
10X single cell sequencing issue
Can you please help me in a technical issue? We sent some samples to single cell sequencing The company says
Many of the reads were not assigned to cell-associated barcodes. This
could be caused by ...
-5
votes
1answer
89 views
Making Seurat object from a processed file [closed]
I have downloaded log2(TPM/10+1) values of 11,548 genes and 9609 cells from ...
-1
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1answer
171 views
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45 views
which marker identifications method is recommended when single-nuclei RNA seq datasets are integrated across regions
I'm analyzing Sn-RNA seq datasets which include different brain regions and spinal cord in patients and normal controls. I would have different comparison within and between individuals. I've got a ...
0
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2answers
85 views
cellranger mkfastq with full path to --id flag
I have always used cellranger mkfastq to demultiplex 10x genomics runs manually, though recently the commands to do so have been incorporated into a script that ...
1
vote
1answer
1k views
Reading multiple raw files in Seurat
I have multiple single cell samples to analyze and I'm following the instructions in Satija Lab's website. I want to merge all the count files from all the samples at once, and associate the metadata ...
0
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1answer
167 views
Single-cell sequencing dataset has too many barcodes
I am analyzing a single-cell sequencing dataset from the website 10xgenomics, with 2000 cells. It is a BAM file and I am trying to obtain the individual cells per sample. I used the command
...
3
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0answers
542 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 ...
4
votes
2answers
195 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 ...
2
votes
1answer
781 views
Why do I have >10,000 cells in the 10X matrix produced by cellranger?
In my scRNA seq experiment, single-cell libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3′ Library & Gel Bead Kit v2 and Chip Kit (10x Genomics) according to the ...
5
votes
2answers
1k views
BAM to gene expression matrix (UMI counts per gene per cell),10X
I am trying to reproduce some results of a scRNASeq experiment. However I am new to the server-side aspect of such analyses and am very confused at the moment.
The data provided by the authors of the ...
5
votes
1answer
787 views
How to normalise scRNASeq data for differential expression analysis
I wish to perform differential expression analysis for cluster-specific gene expression in single-cell data (with a tool such as MAST or SCDE).
I have data for 3 biological replicates. I performed ...
2
votes
4answers
2k views
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 ...
5
votes
1answer
673 views
Derive a GTF containing protein coding genes from a GTF file with Exons and CDS
Why I need a compatible file
I’m trying to run
velocyto with the R package to analyse RNA velocity (cell trajectories) with single cell RNASeq data. I have performed single cell analysis from 10x ...
2
votes
2answers
246 views
Can I get the graph generated by cellranger
I’ve run the cellranger analysis pipeline on single cell RNASeq datasets. I can import the matrix and graph-based clusters into R. Doing this I can optimise the dimension reduction and plot cells with ...
5
votes
3answers
7k views
Script to allow gene set enrichment analysis of 10x genomics data in R
I have 10x single cell RNA seq data. Which R package is best suited for analysis of the 10x data matrix. What is the script to prepare the data for downstream GSEA analysis.
I have already processed ...
2
votes
1answer
1k views
Why are there more barcodes than GEMs in 10X chromium data?
Question: Why are there more barcodes than GEMs in 10X chromium data?
Introduction
I have several 10X genomics chromium libraries made with the de novo assembly/genome protocol. The 10X chromium ...
9
votes
3answers
6k views
What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?
What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.)
For example, I recently received some 10X ...
1
vote
1answer
159 views
How to search a specific sequence in BAM files for 10X experiment
I have to search a specific sequence in a set of cells (> 1k cells) from a single-cell experiment done with 10X genomics.
As input file I have a single bam file, and 24 fastqs, therefore each file ...
4
votes
1answer
2k views
Raw vs Filtered in the output of cellranger count
After running cellranger count I got two relevant for further analysis folders: filtered_gene_bc_matrices and ...
4
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2answers
2k views
What is cellranger doing in comparison to other methods?
I've recently started working with the 10X-Genomics platform with Illumina (MiSeq and HiSeq) for single-cell RNA-Seq. I've been recommended the "cellranger" (version 2.1.0) which I understand handles ...
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1answer
2k views
10X cellranger count, [error] The chemistry was unable to be automatically determined
While running cellranger count using the following .slurm file:
...
3
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2answers
2k views
10X Illumina demultiplexing sample sheet issue
Also posted on biostars.
I am trying to use cellranger or bcl2fastq to convert the .bcl ...
12
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2answers
3k views
determining doublets in single-cell RNA-seq
Doublets are a known problem with scRNA-seq experiments, where 2 or more cells are sometimes captured instead. To determine their presence, there are studies that mix multiple species (such as human ...
3
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2answers
2k views
Handling sample identity in aggregated 10x libraries?
cellranger aggr can combine multiple libraries (samples), and appends each barcode with an integer (e.g. AGACCATTGAGACTTA-1). The sample identity is not recorded in ...
4
votes
1answer
2k views
10x Genomics Chromium single-cell RNA-seq data analysis options?
Provide an overview of 10x data analysis packages.
10x provides Cell Ranger which prepares a count matrix from the bcl sequencer output files and other files (see bottom of page https://support....
6
votes
1answer
207 views
Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?
I got a customized GRCh38.79 .gtf file (modified to have no MT genes) and I need to create a reference genome out of it (for 10xGenomics CellRanger pipeline). I suspect that the .79 part is the ...
