6/
Today, I ask AI to explain it like I’m 5.
And then I go deeper myself.
Here’s my full post on that before AI was available and I spent many hours to figure it out:
divingintogeneticsandgenomics.com/post/calcul...
Today, I ask AI to explain it like I’m 5.
And then I go deeper myself.
Here’s my full post on that before AI was available and I spent many hours to figure it out:
divingintogeneticsandgenomics.com/post/calcul...
Calculate scATACseq TSS enrichment score | Chatomics
TSS enrichment score serves as an important quality control metric for ATACseq data. I want to write a script for single cell ATACseq data.
From the Encode page:
Transcription Start Site (TSS) Enrichment Score - The TSS enrichment calculation is a signal to noise calculation. The reads around a reference set of TSSs are collected to form an aggregate distribution of reads centered on the TSSs and extending to 1000 bp in either direction (for a total of 2000bp).
divingintogeneticsandgenomics.com
October 31, 2026 at 1:15 PM
6/
Today, I ask AI to explain it like I’m 5.
And then I go deeper myself.
Here’s my full post on that before AI was available and I spent many hours to figure it out:
divingintogeneticsandgenomics.com/post/calcul...
Today, I ask AI to explain it like I’m 5.
And then I go deeper myself.
Here’s my full post on that before AI was available and I spent many hours to figure it out:
divingintogeneticsandgenomics.com/post/calcul...
Mehta et al. combine ATACseq/RNAseq of multiple cichlids to show that many regulatory “switches” are both deeply conserved and rapidly changing, and that small DNA changes in these regions can alter when and where key genes are turned on.
🔗️ academic.oup.com/gbe/article/...
#societyjournal #genome
🔗️ academic.oup.com/gbe/article/...
#societyjournal #genome
October 29, 2026 at 10:01 AM
Mehta et al. combine ATACseq/RNAseq of multiple cichlids to show that many regulatory “switches” are both deeply conserved and rapidly changing, and that small DNA changes in these regions can alter when and where key genes are turned on.
🔗️ academic.oup.com/gbe/article/...
#societyjournal #genome
🔗️ academic.oup.com/gbe/article/...
#societyjournal #genome
10/
Want to learn it?
Here's my tutorial with code, real examples, and best practices:
divingintogeneticsandgenomics.com/post/use-do...
Want to learn it?
Here's my tutorial with code, real examples, and best practices:
divingintogeneticsandgenomics.com/post/use-do...
Use docopt to write command line R utilities | Chatomics
I was writing an R script to plot the ATACseq fragment length distribution and wanted to turn the R script to a command line utility.
I then (re)discovered this awesome docopt.R. One just needs to write the help message the you want to display and docopt() will parse the options, arguments and return a named list which can be accessed inside the R script. check http://docopt.org/ for more information as well.
divingintogeneticsandgenomics.com
October 30, 2026 at 1:45 PM
10/
Want to learn it?
Here's my tutorial with code, real examples, and best practices:
divingintogeneticsandgenomics.com/post/use-do...
Want to learn it?
Here's my tutorial with code, real examples, and best practices:
divingintogeneticsandgenomics.com/post/use-do...
New ATAC-seq products and services are here, from competitor-benchmarked reagents to full-service chromatin accessibility profiling.
At #ASHG26? Visit booth 416 to talk ATAC-seq and more with our team.
🔗https://ow.ly/JYH750ZZxoE
#ATACseq
At #ASHG26? Visit booth 416 to talk ATAC-seq and more with our team.
🔗https://ow.ly/JYH750ZZxoE
#ATACseq
October 21, 2026 at 6:00 PM
New ATAC-seq products and services are here, from competitor-benchmarked reagents to full-service chromatin accessibility profiling.
At #ASHG26? Visit booth 416 to talk ATAC-seq and more with our team.
🔗https://ow.ly/JYH750ZZxoE
#ATACseq
At #ASHG26? Visit booth 416 to talk ATAC-seq and more with our team.
🔗https://ow.ly/JYH750ZZxoE
#ATACseq
In both crickets and crustaceans, the regulatory elements that become active are enriched in binding motifs for Zelda. This pioneer transcription factor is already well known in flies, where it it selects the first zygotic genes to be activated in early embryos.
October 17, 2026 at 9:42 AM
In both crickets and crustaceans, the regulatory elements that become active are enriched in binding motifs for Zelda. This pioneer transcription factor is already well known in flies, where it it selects the first zygotic genes to be activated in early embryos.
Intelligent Compute delivered on average:
✅ 59-86% lower costs
✅ 42-55% fewer CPU hours
✅ 16-49% faster wallclock time
🔗 Read the benchmarks blog: hubs.la/Q04Bgrl10
✅ 59-86% lower costs
✅ 42-55% fewer CPU hours
✅ 16-49% faster wallclock time
🔗 Read the benchmarks blog: hubs.la/Q04Bgrl10
Benchmarking Seqera Intelligent Compute on AWS, Azure and Google Cloud: nf-core Pipeline Results
We comparing Intelligent Compute with Azure Batch and Google Cloud Batch across seven nf-core pipelines: rnaseq, sarek, atacseq, chipseq, nanoseq, and viralrecon.
hubs.la
October 15, 2026 at 1:41 PM
Intelligent Compute delivered on average:
✅ 59-86% lower costs
✅ 42-55% fewer CPU hours
✅ 16-49% faster wallclock time
🔗 Read the benchmarks blog: hubs.la/Q04Bgrl10
✅ 59-86% lower costs
✅ 42-55% fewer CPU hours
✅ 16-49% faster wallclock time
🔗 Read the benchmarks blog: hubs.la/Q04Bgrl10
Seqera Intelligent Compute is a new-generation compute service that abstracts away the complexity of scaling @nextflow.io pipelines in the cloud.☁️We benchmarked it against the native batch services of AWS, Azure and Google Cloud using popular @nf-co.re pipelines.🧵 hubs.la/Q04Bgrl10
Benchmarking Seqera Intelligent Compute on AWS, Azure and Google Cloud: nf-core Pipeline Results
We comparing Intelligent Compute with Azure Batch and Google Cloud Batch across seven nf-core pipelines: rnaseq, sarek, atacseq, chipseq, nanoseq, and viralrecon.
hubs.la
October 15, 2026 at 1:41 PM
Seqera Intelligent Compute is a new-generation compute service that abstracts away the complexity of scaling @nextflow.io pipelines in the cloud.☁️We benchmarked it against the native batch services of AWS, Azure and Google Cloud using popular @nf-co.re pipelines.🧵 hubs.la/Q04Bgrl10
Stop paying for wasted resources.💡Michael Tansini just showed how @seqera.io Intelligent Compute can significantly cut costs, benchmarked on real @nf-co.re pipelines. Now expanded to Azure and GCP!📕 Learn more: hubs.la/Q04B63F40 #NextflowSummit
Benchmarking Seqera Intelligent Compute on AWS, Azure and Google Cloud: nf-core Pipeline Results
We comparing Intelligent Compute with Azure Batch and Google Cloud Batch across seven nf-core pipelines: rnaseq, sarek, atacseq, chipseq, nanoseq, and viralrecon.
hubs.la
October 14, 2026 at 12:03 PM
Stop paying for wasted resources.💡Michael Tansini just showed how @seqera.io Intelligent Compute can significantly cut costs, benchmarked on real @nf-co.re pipelines. Now expanded to Azure and GCP!📕 Learn more: hubs.la/Q04B63F40 #NextflowSummit
CUTANA™ ATAC-seq Services
Send us your samples and let our chromatin mapping experts manage your ATAC-seq project from experimental design through personalized data delivery.
🔗 https://ow.ly/HSHf50ZVrIC
#ATACseq #Epigenomics #ChromatinAccessibility #Genomics #GenomicServices
Send us your samples and let our chromatin mapping experts manage your ATAC-seq project from experimental design through personalized data delivery.
🔗 https://ow.ly/HSHf50ZVrIC
#ATACseq #Epigenomics #ChromatinAccessibility #Genomics #GenomicServices
October 8, 2026 at 2:10 PM
CUTANA™ ATAC-seq Services
Send us your samples and let our chromatin mapping experts manage your ATAC-seq project from experimental design through personalized data delivery.
🔗 https://ow.ly/HSHf50ZVrIC
#ATACseq #Epigenomics #ChromatinAccessibility #Genomics #GenomicServices
Send us your samples and let our chromatin mapping experts manage your ATAC-seq project from experimental design through personalized data delivery.
🔗 https://ow.ly/HSHf50ZVrIC
#ATACseq #Epigenomics #ChromatinAccessibility #Genomics #GenomicServices
Our expansion of single-cell epigenetics assays continues!
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
October 1, 2026 at 7:32 PM
Our expansion of single-cell epigenetics assays continues!
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
A cost-effective method for finding cis-regulatory elements in a large genome (Parhyale, 3.6 Gb), combining info from chromatin accessibility (bulk & single-nucleus ATACseq) and cross-species sequence conservation (low coverage sequencing from 3 additional Parhyale species)
Now published in eLife!
Now published in eLife!
Genome-wide discovery of cis-regulatory elements in a large genome
Integrating genome-wide maps of chromatin accessibility and sequence conservation provides an accessible low-cost approach for identifying cis-regulatory elements in large genomes, validated in the em...
elifesciences.org
October 1, 2026 at 4:38 PM
A cost-effective method for finding cis-regulatory elements in a large genome (Parhyale, 3.6 Gb), combining info from chromatin accessibility (bulk & single-nucleus ATACseq) and cross-species sequence conservation (low coverage sequencing from 3 additional Parhyale species)
Now published in eLife!
Now published in eLife!
How does our new CUTANA™ Tn5 Transposome perform head-to-head in ATAC-seq?
In direct benchmarking, CUTANA™ Tn5 matched a leading competitor enzyme for peak position and shape, TSS enrichment, and signal at shared peaks.
See all the data ⤵️
https://ow.ly/aBtB50ZReta
#ATACseq
In direct benchmarking, CUTANA™ Tn5 matched a leading competitor enzyme for peak position and shape, TSS enrichment, and signal at shared peaks.
See all the data ⤵️
https://ow.ly/aBtB50ZReta
#ATACseq
September 30, 2026 at 2:10 PM
How does our new CUTANA™ Tn5 Transposome perform head-to-head in ATAC-seq?
In direct benchmarking, CUTANA™ Tn5 matched a leading competitor enzyme for peak position and shape, TSS enrichment, and signal at shared peaks.
See all the data ⤵️
https://ow.ly/aBtB50ZReta
#ATACseq
In direct benchmarking, CUTANA™ Tn5 matched a leading competitor enzyme for peak position and shape, TSS enrichment, and signal at shared peaks.
See all the data ⤵️
https://ow.ly/aBtB50ZReta
#ATACseq
How does our new CUTANA™ ATAC-seq Kit perform?
In head-to-head testing the CUTANA™ ATAC-seq Kit maintained peak signal and TSS enrichment across every input tested, while a leading competitor’s kit weakened progressively.
Explore data here: https://ow.ly/vgh550ZQNYS
#ATACseq
In head-to-head testing the CUTANA™ ATAC-seq Kit maintained peak signal and TSS enrichment across every input tested, while a leading competitor’s kit weakened progressively.
Explore data here: https://ow.ly/vgh550ZQNYS
#ATACseq
September 24, 2026 at 1:55 PM
How does our new CUTANA™ ATAC-seq Kit perform?
In head-to-head testing the CUTANA™ ATAC-seq Kit maintained peak signal and TSS enrichment across every input tested, while a leading competitor’s kit weakened progressively.
Explore data here: https://ow.ly/vgh550ZQNYS
#ATACseq
In head-to-head testing the CUTANA™ ATAC-seq Kit maintained peak signal and TSS enrichment across every input tested, while a leading competitor’s kit weakened progressively.
Explore data here: https://ow.ly/vgh550ZQNYS
#ATACseq
6/ 📖 Read the full article:
MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics
🔗 academic.oup.com/gpb/advance-...
💻 MACS3: github.com/macs3-projec...
#Bioinformatics #Epigenomics #SingleCell #ATACseq #ChIPseq #RegulatoryGenomics
MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics
🔗 academic.oup.com/gpb/advance-...
💻 MACS3: github.com/macs3-projec...
#Bioinformatics #Epigenomics #SingleCell #ATACseq #ChIPseq #RegulatoryGenomics
MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics
Abstract. Since the original publication of Model-based Analysis for ChIP-Seq (MACS), the software has been widely used to identify enriched genomic region
academic.oup.com
September 18, 2026 at 12:14 PM
6/ 📖 Read the full article:
MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics
🔗 academic.oup.com/gpb/advance-...
💻 MACS3: github.com/macs3-projec...
#Bioinformatics #Epigenomics #SingleCell #ATACseq #ChIPseq #RegulatoryGenomics
MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics
🔗 academic.oup.com/gpb/advance-...
💻 MACS3: github.com/macs3-projec...
#Bioinformatics #Epigenomics #SingleCell #ATACseq #ChIPseq #RegulatoryGenomics
Introducing the new 🧬CUTANA™ ATAC-seq🧬 portfolio from EpiCypher!
Explore our new ATAC-seq solutions:
📦 ATAC-seq Kit
🧬 Tn5 Transposome
👩🔬 ATAC-seq Services
🔗 Products: epicypher.com/products/atac-seq/
🔗 Services: epicypher.com/services/cutana-atac-seq-services/
#ATACseq #ChromatinAccessibility
Explore our new ATAC-seq solutions:
📦 ATAC-seq Kit
🧬 Tn5 Transposome
👩🔬 ATAC-seq Services
🔗 Products: epicypher.com/products/atac-seq/
🔗 Services: epicypher.com/services/cutana-atac-seq-services/
#ATACseq #ChromatinAccessibility
September 15, 2026 at 3:40 PM
Introducing the new 🧬CUTANA™ ATAC-seq🧬 portfolio from EpiCypher!
Explore our new ATAC-seq solutions:
📦 ATAC-seq Kit
🧬 Tn5 Transposome
👩🔬 ATAC-seq Services
🔗 Products: epicypher.com/products/atac-seq/
🔗 Services: epicypher.com/services/cutana-atac-seq-services/
#ATACseq #ChromatinAccessibility
Explore our new ATAC-seq solutions:
📦 ATAC-seq Kit
🧬 Tn5 Transposome
👩🔬 ATAC-seq Services
🔗 Products: epicypher.com/products/atac-seq/
🔗 Services: epicypher.com/services/cutana-atac-seq-services/
#ATACseq #ChromatinAccessibility
Our expansion of single-cell epigenetics assays continues!
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
September 11, 2026 at 6:52 PM
Our expansion of single-cell epigenetics assays continues!
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
Extract: The Arlotta lab seeks a Postdoctoral Fellow for computational analysis of functional genomics datasets, focusing on brain disorders. The role involves developing methods for RNAseq, ATACseq, and Spatial Transcriptomics datasets.
August 30, 2026 at 4:44 PM
Extract: The Arlotta lab seeks a Postdoctoral Fellow for computational analysis of functional genomics datasets, focusing on brain disorders. The role involves developing methods for RNAseq, ATACseq, and Spatial Transcriptomics datasets.
Sharing a new preprint about technical variation in (bulk/ #SingleCell ) #ATACseq and motif accessibility analyses, and methods to correct for them www.biorxiv.org/content/10.6...
August 26, 2026 at 7:32 AM
Sharing a new preprint about technical variation in (bulk/ #SingleCell ) #ATACseq and motif accessibility analyses, and methods to correct for them www.biorxiv.org/content/10.6...
6/
Today, I ask AI to explain it like I’m 5.
And then I go deeper myself.
Here’s my full post on that before AI was available and I spent many hours to figure it out:
divingintogeneticsandgenomics.com/post/calcul...
Today, I ask AI to explain it like I’m 5.
And then I go deeper myself.
Here’s my full post on that before AI was available and I spent many hours to figure it out:
divingintogeneticsandgenomics.com/post/calcul...
Calculate scATACseq TSS enrichment score | Chatomics
TSS enrichment score serves as an important quality control metric for ATACseq data. I want to write a script for single cell ATACseq data.
From the Encode page:
Transcription Start Site (TSS) Enrichment Score - The TSS enrichment calculation is a signal to noise calculation. The reads around a reference set of TSSs are collected to form an aggregate distribution of reads centered on the TSSs and extending to 1000 bp in either direction (for a total of 2000bp).
divingintogeneticsandgenomics.com
August 23, 2026 at 1:15 PM
6/
Today, I ask AI to explain it like I’m 5.
And then I go deeper myself.
Here’s my full post on that before AI was available and I spent many hours to figure it out:
divingintogeneticsandgenomics.com/post/calcul...
Today, I ask AI to explain it like I’m 5.
And then I go deeper myself.
Here’s my full post on that before AI was available and I spent many hours to figure it out:
divingintogeneticsandgenomics.com/post/calcul...
Our expansion of single-cell epigenetics assays continues!
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
August 13, 2026 at 8:01 PM
Our expansion of single-cell epigenetics assays continues!
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
The Epigenome Technologies scCUT&Tag assay is now compatible with the BD Rhapsody platform
#Epigenetics #BDrhapsody #CUTandTag #Chromatin #Multiomics #Singlecell #CUTandRUN #ChIPseq #ATACseq
Learn more here: u.epigenome.us/NYjSGQao
Postdoc opportunities in the comparative analysis of planarian regeneration!
We’ve got a worm Zoo and high-quality genomes; we need you to explore gene regulatory mechanisms by scSeq, CHIP/ATACseq and/or comparative genomics
Questions? Please PM
Please RT
We’ve got a worm Zoo and high-quality genomes; we need you to explore gene regulatory mechanisms by scSeq, CHIP/ATACseq and/or comparative genomics
Questions? Please PM
Please RT
August 14, 2026 at 4:17 PM
Postdoc opportunities in the comparative analysis of planarian regeneration!
We’ve got a worm Zoo and high-quality genomes; we need you to explore gene regulatory mechanisms by scSeq, CHIP/ATACseq and/or comparative genomics
Questions? Please PM
Please RT
We’ve got a worm Zoo and high-quality genomes; we need you to explore gene regulatory mechanisms by scSeq, CHIP/ATACseq and/or comparative genomics
Questions? Please PM
Please RT
Great conversations and inspiring vibes at @events.embl.org — felt amazing to share my work and hear from incredible speakers!
#EESAgeing #SingleCell #Aging #ATACseq #RNAseq #Immunology #Multiomics #scRNAseq #scATACseq
#EESAgeing #SingleCell #Aging #ATACseq #RNAseq #Immunology #Multiomics #scRNAseq #scATACseq
June 11, 2025 at 3:45 PM
Great conversations and inspiring vibes at @events.embl.org — felt amazing to share my work and hear from incredible speakers!
#EESAgeing #SingleCell #Aging #ATACseq #RNAseq #Immunology #Multiomics #scRNAseq #scATACseq
#EESAgeing #SingleCell #Aging #ATACseq #RNAseq #Immunology #Multiomics #scRNAseq #scATACseq
Join us for our July #webinar, where Armaan will cover an overview of #epigenetics, how to incorporate #ChIPseq, #RIPseq, #ATACseq, #EMseq and DNA #methylation in your own epigenetics projects.
Register here: bit.ly/4e25SUe
#novogene #nextgenerationsequencing #ngs
Register here: bit.ly/4e25SUe
#novogene #nextgenerationsequencing #ngs
June 10, 2025 at 12:47 PM
Join us for our July #webinar, where Armaan will cover an overview of #epigenetics, how to incorporate #ChIPseq, #RIPseq, #ATACseq, #EMseq and DNA #methylation in your own epigenetics projects.
Register here: bit.ly/4e25SUe
#novogene #nextgenerationsequencing #ngs
Register here: bit.ly/4e25SUe
#novogene #nextgenerationsequencing #ngs
Also, all data we have generated (WGS, RNA-seq, ATAC-seq and methylation) is available at the European Genome-phenome Archive (EGA)
ega-archive.org/datasets/EGA...
ega-archive.org/datasets/EGA...
ega-archive.org/datasets/EGA...
ega-archive.org/datasets/EGA...
WGS, RNAseq and ATACseq data for the validation of an iPSC model of MPNST progression - EGA European Genome-Phenome Archive
WGS, RNA-seq and ATAC-seq data for the validation of an iPSC model of MPNST progression. It includes the cells of the model (1KO, 2KO and 3KO) at various differ
ega-archive.org
June 22, 2026 at 11:11 AM
Also, all data we have generated (WGS, RNA-seq, ATAC-seq and methylation) is available at the European Genome-phenome Archive (EGA)
ega-archive.org/datasets/EGA...
ega-archive.org/datasets/EGA...
ega-archive.org/datasets/EGA...
ega-archive.org/datasets/EGA...