CellRanger v9.0 was released on Nov. 18th. Looking through changes:
"Starting with v9.0, anonymized telemetry data is collected and sent to 10x Genomics" 👀
"Starting with v9.0, anonymized telemetry data is collected and sent to 10x Genomics" 👀
November 26, 2024 at 2:51 AM
CellRanger v9.0 was released on Nov. 18th. Looking through changes:
"Starting with v9.0, anonymized telemetry data is collected and sent to 10x Genomics" 👀
"Starting with v9.0, anonymized telemetry data is collected and sent to 10x Genomics" 👀
Mark(@sanbomics.bsky.social) put together a really nice video & walkthrough on using alevin-fry/simpleAF to process your single-cell RNA-seq data. If you're doing processing of such data, I recommend checking it out as a transparent & open alternative to CellRanger (& way faster) t.co/Hu9ueRduQ9! 🖥️🧬
Processing single-cell RNAseq counts with simpleaf (alevin-fry)
Simpleaf is a faster and more efficient alternative to other counters, such as cellranger, and it works with other single-cell chemistries. It is a wrapper f...
t.co
September 15, 2023 at 1:16 PM
Mark(@sanbomics.bsky.social) put together a really nice video & walkthrough on using alevin-fry/simpleAF to process your single-cell RNA-seq data. If you're doing processing of such data, I recommend checking it out as a transparent & open alternative to CellRanger (& way faster) t.co/Hu9ueRduQ9! 🖥️🧬
The truly open solution is the technicallu better one here (SLOW5). Even if it was not, there would be strong reasons to prefer it. I hope the community rejects closed or strangely licensed basic tools, not just POD5, but also pseudo-open offerings like CellRanger. Good alternatives exist!
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data https://www.biorxiv.org/content/10.1101/2025.06.30.662478v1
July 4, 2025 at 9:08 PM
The truly open solution is the technicallu better one here (SLOW5). Even if it was not, there would be strong reasons to prefer it. I hope the community rejects closed or strangely licensed basic tools, not just POD5, but also pseudo-open offerings like CellRanger. Good alternatives exist!
Hi ! I am new here and I like to present my interests with this video from our Journal Club! This is an overview of the multiome analysis for scATACseq and scRNAseq using several
#CellRanger pipelines. This is inspired by our work at #LIBD and resources from 10x Genomics. youtu.be/fHVLi9-sftM?...
#CellRanger pipelines. This is inspired by our work at #LIBD and resources from 10x Genomics. youtu.be/fHVLi9-sftM?...
[2024-10-11] An overview of the CellRanger-ARC Pipeline Analysis
YouTube video by Leonardo Collado Torres
youtu.be
November 8, 2024 at 8:29 PM
Hi ! I am new here and I like to present my interests with this video from our Journal Club! This is an overview of the multiome analysis for scATACseq and scRNAseq using several
#CellRanger pipelines. This is inspired by our work at #LIBD and resources from 10x Genomics. youtu.be/fHVLi9-sftM?...
#CellRanger pipelines. This is inspired by our work at #LIBD and resources from 10x Genomics. youtu.be/fHVLi9-sftM?...
Reframe cellranger as an alternative, closed version of alevin-fry/simpleAF. We need reframe the conversation to have the open versions be the de facto and closed versions as alternatives. Cellranger is a major pain to get working in an automated pipeline due to its closed source and license.
September 15, 2023 at 3:06 PM
Reframe cellranger as an alternative, closed version of alevin-fry/simpleAF. We need reframe the conversation to have the open versions be the de facto and closed versions as alternatives. Cellranger is a major pain to get working in an automated pipeline due to its closed source and license.
One way we made it fast was by mapping with simpleaf (github.com/COMBINE-lab/...) 🥳 This gives a ~50x speed-up over CellRanger, and natively produces spliced vs unspliced reads. Percent spliced reads is IMO *the* most important QC metric for single nuclei data (link.springer.com/article/10.1...).
GitHub - COMBINE-lab/simpleaf: A rust framework to make using alevin-fry even simpler
A rust framework to make using alevin-fry even simpler - COMBINE-lab/simpleaf
github.com
March 13, 2026 at 6:02 PM
One way we made it fast was by mapping with simpleaf (github.com/COMBINE-lab/...) 🥳 This gives a ~50x speed-up over CellRanger, and natively produces spliced vs unspliced reads. Percent spliced reads is IMO *the* most important QC metric for single nuclei data (link.springer.com/article/10.1...).
It is by default "ON", which is the opposite of what I would have recommended.
It can be disabled by:
```cellranger telemetry disable```
or
```export TENX_DISABLE_TELEMETRY=1``` in the environment settings
It can be disabled by:
```cellranger telemetry disable```
or
```export TENX_DISABLE_TELEMETRY=1``` in the environment settings
November 26, 2024 at 1:45 PM
It is by default "ON", which is the opposite of what I would have recommended.
It can be disabled by:
```cellranger telemetry disable```
or
```export TENX_DISABLE_TELEMETRY=1``` in the environment settings
It can be disabled by:
```cellranger telemetry disable```
or
```export TENX_DISABLE_TELEMETRY=1``` in the environment settings
TBH alternatives to cellranger have been around for a while, chromap or sinto to name a couple. Yet, it’s worth trying this one.
December 4, 2024 at 5:02 PM
TBH alternatives to cellranger have been around for a while, chromap or sinto to name a couple. Yet, it’s worth trying this one.
We're looking for a publicly available 10x Flex v2 gene expression dataset to test out our simpleaf pipeline on (we need raw FASTQ data and, ideally, CellRanger count matrices). Unfortunately, 10x only has Flex v1 data available on their website, and the v2 chemistry is different. Any ideas?
March 20, 2026 at 4:36 PM
We're looking for a publicly available 10x Flex v2 gene expression dataset to test out our simpleaf pipeline on (we need raw FASTQ data and, ideally, CellRanger count matrices). Unfortunately, 10x only has Flex v1 data available on their website, and the v2 chemistry is different. Any ideas?
10X Genomics just made the source for CellRanger available (but not open source); github.com/10XGenomics/...! While I strongly advocate for using truly open tools for sc preprocessing e.g. github.com/COMBINE-lab/..., this is still a huge win for computational transparency in single cell analysis! 🖥️🧬
GitHub - COMBINE-lab/simpleaf: A rust framework to make using alevin-fry even simpler
A rust framework to make using alevin-fry even simpler - GitHub - COMBINE-lab/simpleaf: A rust framework to make using alevin-fry even simpler
github.com
November 10, 2023 at 8:05 PM
10X Genomics just made the source for CellRanger available (but not open source); github.com/10XGenomics/...! While I strongly advocate for using truly open tools for sc preprocessing e.g. github.com/COMBINE-lab/..., this is still a huge win for computational transparency in single cell analysis! 🖥️🧬
This is a very cool demonstration of the possibilities of 10x Flex link.springer.com/article/10.1...! But did you know that you can get near identical results MANY TIMES faster than CellRanger by processing flex data with piscem/alevin-fry or cyto? Both highly efficient & fully, truly open source?/2
10 × Genomics Flex Gene Expression is a powerful tool for single-cell transcriptomics of xenografts models - Genome Biology
The 10 × Genomics Flex Gene Expression protocol is a probe-based method that profiles fixed or frozen material, simplifying sample handling before scRNA-seq. Although probes exist only for human and m...
link.springer.com
May 11, 2026 at 11:31 AM
This is a very cool demonstration of the possibilities of 10x Flex link.springer.com/article/10.1...! But did you know that you can get near identical results MANY TIMES faster than CellRanger by processing flex data with piscem/alevin-fry or cyto? Both highly efficient & fully, truly open source?/2
This sort of thing is disturbingly common. Cellranger, epi2me (at least the workflows I’ve seen), even blast sends back usage info unless you block it.
November 26, 2024 at 7:11 AM
This sort of thing is disturbingly common. Cellranger, epi2me (at least the workflows I’ve seen), even blast sends back usage info unless you block it.
The more truly open alternatives we have to CellRanger, the better! This is especially true if they are resource efficient & we can integrate them into the same core tool ecosystem. We will be working on upstream support for simpleaf soon to simplify scATAC preproc, and to codify best practices. 3/3
December 2, 2024 at 11:25 PM
The more truly open alternatives we have to CellRanger, the better! This is especially true if they are resource efficient & we can integrate them into the same core tool ecosystem. We will be working on upstream support for simpleaf soon to simplify scATAC preproc, and to codify best practices. 3/3
Currently the only tool that supports this data type is CellRanger and we show that cyto provides runtimes an order of magnitude faster (16x), uses less than half the memory, dramatically reduces CPU-hours (30x) and reduces total IO by more than 5x.
January 22, 2026 at 5:23 PM
Currently the only tool that supports this data type is CellRanger and we show that cyto provides runtimes an order of magnitude faster (16x), uses less than half the memory, dramatically reduces CPU-hours (30x) and reduces total IO by more than 5x.
Running cellranger on Amarel
For 10X scRNAseq experiments, you can process fastq files on the Rutgers Amarel HPC system using the pre-installed cellranger software package. Here's how. Cellranger is available from the "community" modules, so first you'll need to add these to the standard list of…
For 10X scRNAseq experiments, you can process fastq files on the Rutgers Amarel HPC system using the pre-installed cellranger software package. Here's how. Cellranger is available from the "community" modules, so first you'll need to add these to the standard list of…
Running cellranger on Amarel
For 10X scRNAseq experiments, you can process fastq files on the Rutgers Amarel HPC system using the pre-installed cellranger software package. Here's how. Cellranger is available from the "community" modules, so first you'll need to add these to the standard list of modules. module use /projects/community/modulefiles The pre-installed module may not be the current version of the software. To see which versions are loaded, type:
njstem.wordpress.com
February 4, 2025 at 7:40 PM
Running cellranger on Amarel
For 10X scRNAseq experiments, you can process fastq files on the Rutgers Amarel HPC system using the pre-installed cellranger software package. Here's how. Cellranger is available from the "community" modules, so first you'll need to add these to the standard list of…
For 10X scRNAseq experiments, you can process fastq files on the Rutgers Amarel HPC system using the pre-installed cellranger software package. Here's how. Cellranger is available from the "community" modules, so first you'll need to add these to the standard list of…
I think you can also tell cellranger to skip file preflight checks
December 16, 2024 at 6:09 PM
I think you can also tell cellranger to skip file preflight checks
This required tons of new software, all of which we've made available open source. This includes software for single-cell transposon genomics! (CellRanger-TE), Deep ALS Neural Net Classifiers (DANCer) that work on bulk or single-cell data! +more!
www.mghlab.org/software
github.com/mhammell-lab...
www.mghlab.org/software
github.com/mhammell-lab...
MGHammell Laboratory
The Gale Hammell Lab uses algorithms to integrate high throughput sequencing data to model regulatory re-wiring events in human diseases. - MGHammell Laboratory
github.com
March 10, 2025 at 9:49 PM
This required tons of new software, all of which we've made available open source. This includes software for single-cell transposon genomics! (CellRanger-TE), Deep ALS Neural Net Classifiers (DANCer) that work on bulk or single-cell data! +more!
www.mghlab.org/software
github.com/mhammell-lab...
www.mghlab.org/software
github.com/mhammell-lab...
FML. Just pushed the cellranger v8 pipeline to production last week. The grind never ends
And now you can try the automated cell annotation directly in Cell Ranger 9!
www.10xgenomics.com/support/soft...
#singlecell #bioinformatics #genomics
www.10xgenomics.com/support/soft...
#singlecell #bioinformatics #genomics
November 19, 2024 at 8:47 PM
FML. Just pushed the cellranger v8 pipeline to production last week. The grind never ends
📖 Read about Umite, our smart-seq3 UMI counting pipeline: Umite is robust, memory- and time efficient, and outperforms prior tools in UMI retrieval by 10-15 %, and already packaged in a reproducible Snakemake pipeline
🔗 doi.org/qsnx
by Leo Carl Foerster et al.
#umi #smartseq3 #singlecell
🔗 doi.org/qsnx
by Leo Carl Foerster et al.
#umi #smartseq3 #singlecell
Umite: fast quantification of smart-seq3 libraries with improved UMI retrieval
AbstractMotivation. Commercial solutions like 10X cellranger provide robust UMI quantification for their proprietary single-cell protocols, but open method
doi.org
February 24, 2026 at 8:17 AM
📖 Read about Umite, our smart-seq3 UMI counting pipeline: Umite is robust, memory- and time efficient, and outperforms prior tools in UMI retrieval by 10-15 %, and already packaged in a reproducible Snakemake pipeline
🔗 doi.org/qsnx
by Leo Carl Foerster et al.
#umi #smartseq3 #singlecell
🔗 doi.org/qsnx
by Leo Carl Foerster et al.
#umi #smartseq3 #singlecell
scCompBio-BSky: Is there a way to take a 10X BAM file output, give a BED/GTF annotation, and get per-cell count matrix, without going through the "BAM->FASTQ->CellRanger" route (huge files)? I tried "bedtools tag", but it doesn't seem to split the alignment records...
January 11, 2024 at 8:39 AM
scCompBio-BSky: Is there a way to take a 10X BAM file output, give a BED/GTF annotation, and get per-cell count matrix, without going through the "BAM->FASTQ->CellRanger" route (huge files)? I tried "bedtools tag", but it doesn't seem to split the alignment records...
Haven’t read the preprint yet, but if it comes from @robp.bsky.social’s lab, it must be great!
Really nice to see free and open-source alternatives to CellRanger.
Really nice to see free and open-source alternatives to CellRanger.
Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment https://www.biorxiv.org/content/10.1101/2024.11.27.625771v1
December 3, 2024 at 6:42 AM
Haven’t read the preprint yet, but if it comes from @robp.bsky.social’s lab, it must be great!
Really nice to see free and open-source alternatives to CellRanger.
Really nice to see free and open-source alternatives to CellRanger.
When a read has multiple alignments of the same (best) score, the SAM spec doesn't specify any specific rule for which should be designated primary (or even that the rule should be consistent). What does CellRanger do with non-primary alignments 🤔? #singlecell #scrnaseq 🧬🖥
November 23, 2023 at 1:18 AM
When a read has multiple alignments of the same (best) score, the SAM spec doesn't specify any specific rule for which should be designated primary (or even that the rule should be consistent). What does CellRanger do with non-primary alignments 🤔? #singlecell #scrnaseq 🧬🖥
Question: For cellranger-atac count, do we need TWO index files (I1, I2) in addition to two read files (R1, R2)? We're trying to map some public scATAC datasets, and find that sometimes there are two index files deposited (I1 is 8nt, I2 is 16nt), and sometimes only one (eg: ENCODE has only one)...
December 16, 2024 at 5:39 PM
Question: For cellranger-atac count, do we need TWO index files (I1, I2) in addition to two read files (R1, R2)? We're trying to map some public scATAC datasets, and find that sometimes there are two index files deposited (I1 is 8nt, I2 is 16nt), and sometimes only one (eg: ENCODE has only one)...
It's STAR under the hood, and the attached applies, AFAIK. The bam header contains the actual STAR command used, but the older bams I have handy (cellranger 3.0) have `--outSAMmultNmax -1` set, but no other options relevant to multimapping that I see.
November 23, 2023 at 3:14 AM
It's STAR under the hood, and the attached applies, AFAIK. The bam header contains the actual STAR command used, but the older bams I have handy (cellranger 3.0) have `--outSAMmultNmax -1` set, but no other options relevant to multimapping that I see.
Exciting, congrats! Perfect timing for us, I was just looking for non-CellRanger scATAC pipeline options earlier this week! Will have to give it a try....
December 4, 2024 at 4:55 PM
Exciting, congrats! Perfect timing for us, I was just looking for non-CellRanger scATAC pipeline options earlier this week! Will have to give it a try....