Questions tagged [10x-genomics]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1 vote
0 answers
152 views

Loading scATAC-seq data containing matrix.mtx, fragments.tsv and barcodes.tsv files from GEO into R?

I want to analyse the single-cell ATAC-seq data from 10X downloaded from GSE158398. The files attached to this dataset are matrix.mtx.gz, ...
Embla's user avatar
  • 11
1 vote
1 answer
169 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
  • 836
1 vote
1 answer
202 views

In CellRanger output, what are the reads with an xf:i:17 tag?

When running CellRanger on 10x scRNA-Seq data, a BAM file is output with the aligned reads. These reads have an xf tag, described here: The bits of this tag are ...
Alexlok's user avatar
  • 374
2 votes
1 answer
393 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
595 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
0 answers
105 views

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 ...
Angel's user avatar
  • 1,981
0 votes
0 answers
362 views

How to combine multiple .fasta files of primary assembly from Ensembl into one for sequence alignment?

I have some marmoset snRNA reads that I want to align with the reference transcriptome using cellranger. The primary assembly for marmoset is available here, which is broken down into 22 parts. ...
Abhishek Pandey's user avatar
-1 votes
1 answer
77 views

Some definitions about RNA-seq

I want to select a 10x single cell kit What does 2x 50 75 100 150 250 mean in paired end sequencing?
Angel's user avatar
  • 1,981
0 votes
0 answers
965 views

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: ...
mmpp's user avatar
  • 371
1 vote
2 answers
103 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 ...
Angel's user avatar
  • 1,981
0 votes
1 answer
658 views

sctransform - mitochondrial expression filtering / transformation

I have a Seurat object which has a high expression of mitochondrial genes ...
Mahta Mira's user avatar
0 votes
1 answer
2k 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 ...
Mahta Mira's user avatar
2 votes
2 answers
162 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 ...
Mahta Mira's user avatar
1 vote
0 answers
380 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 ...
Mahta Mira's user avatar
0 votes
1 answer
2k views

Seurat heatmap for two conditions

I have a Seurat object of four cancers and four controls ...
Mahta Mira's user avatar
1 vote
2 answers
306 views

Help with Seurat QC ambiguity

I have four PBMC samples from 10X scRNA-seq ...
Mahta Mira's user avatar
1 vote
2 answers
65 views

Merging two dataframes in R

I have a file with cluster number of a scRNA-seq and corresponding annotated cell type like ...
Angel's user avatar
  • 1,981
0 votes
1 answer
523 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 ...
Mahta Mira's user avatar
1 vote
1 answer
64 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 ...
Angel's user avatar
  • 1,981
1 vote
1 answer
924 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: ...
Angel's user avatar
  • 1,981
0 votes
2 answers
140 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 ...
user3377241's user avatar
2 votes
1 answer
2k 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 ...
Angel's user avatar
  • 1,981
2 votes
2 answers
2k 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 ...
Angel's user avatar
  • 1,981
-1 votes
2 answers
268 views

Removing cells zero for a gene from a scRNA-seq data

I have a big single-cell RNA seq data ...
user6517's user avatar
-2 votes
1 answer
316 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 ...
Angel's user avatar
  • 1,981
1 vote
2 answers
730 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 ...
Mahta Mira's user avatar
-4 votes
1 answer
173 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 ...
Angel's user avatar
  • 1,981
0 votes
1 answer
905 views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
Angel's user avatar
  • 1,981
0 votes
0 answers
93 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 ...
Paria's user avatar
  • 1
0 votes
2 answers
187 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 ...
BCArg's user avatar
  • 283
1 vote
1 answer
3k 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 ...
mmpp's user avatar
  • 371
0 votes
1 answer
347 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 ...
captainshidderwins's user avatar
4 votes
0 answers
930 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 ...
gypti's user avatar
  • 41
5 votes
2 answers
454 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 ...
PPK's user avatar
  • 876
2 votes
1 answer
1k 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 ...
user4620's user avatar
5 votes
2 answers
3k 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 ...
h3ab74's user avatar
  • 836
5 votes
1 answer
1k 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 ...
Tom Kelly's user avatar
  • 873
2 votes
4 answers
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 ...
sophia's user avatar
  • 39
5 votes
1 answer
1k 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 ...
Tom Kelly's user avatar
  • 873
2 votes
2 answers
313 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 ...
Tom Kelly's user avatar
  • 873
5 votes
3 answers
8k 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 ...
Jay's user avatar
  • 51
2 votes
1 answer
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 ...
conchoecia's user avatar
  • 3,141
11 votes
3 answers
10k 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 ...
conchoecia's user avatar
  • 3,141
1 vote
1 answer
296 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 ...
gc5's user avatar
  • 1,783
4 votes
1 answer
4k 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 ...
Nikita Vlasenko's user avatar
4 votes
2 answers
3k 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 ...
Tom Kelly's user avatar
  • 873
1 vote
1 answer
3k views

10X cellranger count, [error] The chemistry was unable to be automatically determined

While running cellranger count using the following .slurm file: ...
Nikita Vlasenko's user avatar
3 votes
2 answers
3k views

10X Illumina demultiplexing sample sheet issue

Also posted on biostars. I am trying to use cellranger or bcl2fastq to convert the .bcl ...
Nikita Vlasenko's user avatar
12 votes
2 answers
4k 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 ...
burger's user avatar
  • 2,169
3 votes
2 answers
3k 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 ...
Peter's user avatar
  • 2,624