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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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Cellranger count failed at detect chemistry

I'm using Cellranger for alignment on scRNA-seq data but got the following error message: ...
Tien's user avatar
  • 43
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0 answers
29 views

Cellranger count for more than 20 fastq files

I'm using Cell ranger to perform alignment on scRNA-seq data. I have more than 20 fastq files for it. They are stored in folder test/test_S1_L00XX_R1_001.fastq.gz ...
Tien's user avatar
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1 vote
0 answers
29 views

Large skip after aligning using Cellranger

I have a read from BAM file as following ...
Tien's user avatar
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1 vote
2 answers
28 views

cellranger-arc throws an error when demultiplexing

I have a multiome dataset from a 10x run I'm trying to demultiplex using cellranger-arc mkfastq. The demultiplexing uses the ...
Assa Yeroslaviz's user avatar
2 votes
1 answer
61 views

How to import data from cell ranger to R (Seurat) using Read10X?

I am loading cellranger data into seuratobject as following, but it keeps showing Error in Barcode file missing. Expecting barcodes.tsv.gz the running code and ...
Kent Yang's user avatar
2 votes
2 answers
84 views

problem with running Kallisto on single cell data

I am totally new to bioinformatics, therefore apologies if the terminology is not correct or the question is dumb :) I have been trying the following: installed miniconda create an environment called ...
Simon's user avatar
  • 31
2 votes
0 answers
118 views

Cell Ranger returns too few cells!

I recently performed single cell RNA seq using core services and the web summary output from 10x that they have given shows that there are very few cells detected (100-300) cells per sample. Once this ...
Abhishek Dubey's user avatar
0 votes
3 answers
317 views

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 ...
David's user avatar
  • 1
-1 votes
1 answer
104 views

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 ...
A4747's user avatar
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1 vote
1 answer
530 views

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 ...
Hirak Sarkar's user avatar
1 vote
1 answer
279 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
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1 vote
1 answer
80 views

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 ...
Sam's user avatar
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1 vote
1 answer
388 views

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 ...
Cheng Lyu's user avatar
1 vote
1 answer
332 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
  • 384
1 vote
1 answer
922 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
2 answers
3k views

How to convert 10x matrix.mtx.gz files to hdf5 format?

I have a bunch of folders containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz from the Cellranger Count output for a single-cell dataset that was sent to me from another lab. I need the .h5 ...
Johnny Rocketfingers's user avatar
0 votes
0 answers
402 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
0 votes
1 answer
108 views

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 ...
Alexis Finkbeiner's user avatar
1 vote
2 answers
110 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 ...
Zizogolu's user avatar
  • 2,160
0 votes
2 answers
148 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
0 votes
1 answer
1k views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
Zizogolu's user avatar
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0 votes
2 answers
207 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
0 answers
2k views

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 ...
raiora's user avatar
  • 77
0 votes
1 answer
3k views

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/...
raiora's user avatar
  • 77
0 votes
1 answer
609 views

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 ...
cer's user avatar
  • 105
2 votes
1 answer
300 views

Using cellranger for non-10x data

I'm trying to use cellranger to mkfastq and then count and aggregate single-cell data. This ...
Yuriy Grabovsky's user avatar
0 votes
1 answer
82 views

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 ...
guest's user avatar
  • 1
1 vote
2 answers
656 views

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 ...
sv1234's user avatar
  • 29
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
2 votes
5 answers
3k 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
3 votes
2 answers
2k views

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?
hua's user avatar
  • 441
2 votes
2 answers
334 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
9k 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
5 votes
1 answer
1k views

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 ...
gc5's user avatar
  • 1,813
2 votes
1 answer
949 views

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 ...
Tom Kelly's user avatar
  • 873
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
6 votes
1 answer
244 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 ...
Devon Ryan's user avatar
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