Questions tagged [cellranger]

For questions regarding use of the 10X Genomics' "Cell Ranger" analysis tool for the Chromium single-cell sequencing platform.

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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. ...
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How to solve correlation problems between different samples in scRNA-seq?

I am trying to align and merge different samples from NCBI. I end up having correlation problem with these sample. The picture below shows an heatmap of the R² by doing a linear regression between 2 ...
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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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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 ...
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Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
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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 ...
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10X cellranger error during count

I successfully installed cellranger and performed a test run. Even, I installed bcl2fastq. Everything looked perfect. Thus, I ran cellranger count. I ran into an ...
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Cell Ranger) Error during performing a test run

I am interested in the analysis of single-cell RNA-sequencing data. I installed Cell Ranger according to the instruction (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/...
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Using cellranger mkgtf w/ NCBI GFF3 files

I am using several cellranger tools/pipelines to analyze some data, specifically, mkgtf, mkref, count, and aggr. I am using mkgtf and mkref to include a PI-synthesized protein to my reference. I have ...
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1 answer
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Using cellranger for non-10x data

I'm trying to use cellranger to mkfastq and then count and aggregate single-cell data. This ...
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Clustering using cellranger

Is it possible to run cell ranger clustering using only a gene x cell matrix? Cellranger reanalyze performs clustering but requires a hd5f file. I don't want to run the whole pipeline (including ...
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processing fastq files using cellranger on linux

I am trying to perform a cellranger count on fastq files generated from a 10x genomics single cell RNA Seq run. Just to provide some background, I ssh’d into the AWS using our AWS IP with MobaXTerm ...
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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 ...
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4 answers
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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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  • 39
3 votes
2 answers
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Using Seurat to compare mutant vs.wt

I am interested in using Seurat to compare wild type vs Mutant. I don't know how to use the package. How can I test whether mutant mice, that have deleted gene, cluster together?
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2 answers
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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 ...
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  • 873
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3 answers
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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 ...
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1 answer
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No counts for added gene in cellranger (scRNA-seq)

I have a set of scRNA-seq samples enriched with FACS for cells expressing a specific gene reporter (TdTomato). In particular the gene I want to report has positive counts in the resulting matrix for ...
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What process and input data is required for a cellranger reference transcriptome?

I'm analysing single-cell RNA-Seq data using the 10X Genomics cellranger platform. While they provide reference data for Mouse and Humans, other species require a ...
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  • 873
4 votes
2 answers
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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1 answer
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10X cellranger count, [error] The chemistry was unable to be automatically determined

While running cellranger count using the following .slurm file: ...
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6 votes
1 answer
193 views

Aggregate sequencing/mapping/etc. metrics from cellranger across Illumina samples

I have a number of single-cell projects processed with cellranger from 10x Genomics. The pipeline produces a number of handy metrics that are summarized for each Illumina sample in web page. These ...
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