Questions tagged [10x-genomics]
The 10x-genomics tag has no usage guidance.
40
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39 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
54 views
0
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2answers
50 views
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0answers
26 views
Dimplot does not show the same cell IDs
I have downloaded raw read counts and cell type annotation (cluster number and cell type related to each cell IDs) from a paper
By raw read count I made a seurat object
...
0
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2answers
52 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
35 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
...
0
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1answer
36 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
44 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
votes
1answer
75 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
72 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
votes
2answers
65 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
75 views
-3
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1answer
55 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
votes
2answers
123 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
70 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
71 views
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0answers
32 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
votes
2answers
67 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
851 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
votes
1answer
132 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
...
1
vote
1answer
425 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
138 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
650 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
720 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
3answers
1k views
scRNA-seq,10x cellranger pipelines,low custom tdtomato gene content! looking for help！
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
558 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
225 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
5k 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
147 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
votes
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 ...
0
votes
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
votes
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 ...
11
votes
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
votes
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
197 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 ...
