previous post: chatomics! How to preprocess GEO bulk RNAseq data with salmon divingintogeneticsandgenomics.com/post/how-to...
How to preprocess GEO bulk RNAseq data with salmon | Chatomics
Install fastq-dl To easily download fastq from GEO or ENA, use fastq-dl
Assume you already have conda installed, do the following:
conda config --add channels conda-forge conda config --add channels bioconda conda create -n fastq_download -c conda-forge -c bioconda fastq-dl conda activate fastq_download Tip: use mamba if conda is too slow for you. They are all big snakes!!
We will use bulk RNAseq data from this GEO accession ID: https://www.
divingintogeneticsandgenomics.com
October 28, 2026 at 1:45 PM
previous post: chatomics! How to preprocess GEO bulk RNAseq data with salmon divingintogeneticsandgenomics.com/post/how-to...
🪰 A comparative #RNAseq analysis between #Drosophila males and females identifies female-specific candidate estrogen-related receptor (ERR) targets, where ERR regulates DNA replication and global translation in females.
Find out more in #G3journal 🔗 buff.ly/vltSdR4
@lesleynweaver.bsky.social
Find out more in #G3journal 🔗 buff.ly/vltSdR4
@lesleynweaver.bsky.social
October 28, 2026 at 8:03 PM
🪰 A comparative #RNAseq analysis between #Drosophila males and females identifies female-specific candidate estrogen-related receptor (ERR) targets, where ERR regulates DNA replication and global translation in females.
Find out more in #G3journal 🔗 buff.ly/vltSdR4
@lesleynweaver.bsky.social
Find out more in #G3journal 🔗 buff.ly/vltSdR4
@lesleynweaver.bsky.social
How is your p-value histogram look like? chatomics blog post: Downstream of bulk RNAseq: read in salmon output using tximport and then DESeq2 divingintogeneticsandgenomics.com/post/downst...
October 28, 2026 at 1:45 PM
How is your p-value histogram look like? chatomics blog post: Downstream of bulk RNAseq: read in salmon output using tximport and then DESeq2 divingintogeneticsandgenomics.com/post/downst...
Also a nice blog post!
dave-bridges.blogspot.com/2014/11/vali...
dave-bridges.blogspot.com/2014/11/vali...
Validation of RNAseq Experiments by qPCR?
thoughts on the use of qPCR to validate RNAseq studies
dave-bridges.blogspot.com
October 20, 2026 at 11:21 AM
Also a nice blog post!
dave-bridges.blogspot.com/2014/11/vali...
dave-bridges.blogspot.com/2014/11/vali...
New preprint 📄 Should long-read RNA-seq counts be normalized?
We benchmarked 5 normalization methods × 5 quantifiers on PacBio and ONT, using spike-ins and matched Illumina as ground truth 🧵
www.biorxiv.org/content/10.6...
We benchmarked 5 normalization methods × 5 quantifiers on PacBio and ONT, using spike-ins and matched Illumina as ground truth 🧵
www.biorxiv.org/content/10.6...
Systematic evaluation of transcript normalization methods and quantification pipelines across long-read sequencing platforms
Long-read RNA sequencing (lrRNA-seq) has transformed transcriptomics by enabling full-length isoform resolution, yet transcript quantification remains confounded by platform-dependent length biases an...
www.biorxiv.org
October 19, 2026 at 4:15 PM
New preprint from the Portera-Cailliau lab! Led by the spectacular Michelle W. Wu. During development, cortical activity becomes higher dimensional. PV interneurons (but not SST) drive this shift, and a new circuit model predicts it. Coupled with RNAseq. So happy to have contributed to this work!
Parvalbumin interneuron maturation reorganizes cortical population activity structure during development
During brain development, spontaneous cortical activity undergoes a dramatic transformation from highly synchronous network events to less correlated and sparse neuronal firing that is thought to unde...
www.biorxiv.org
October 23, 2026 at 7:19 PM
New preprint from the Portera-Cailliau lab! Led by the spectacular Michelle W. Wu. During development, cortical activity becomes higher dimensional. PV interneurons (but not SST) drive this shift, and a new circuit model predicts it. Coupled with RNAseq. So happy to have contributed to this work!
Makalede kullanilan rnaseq verilerini kendi pc indirip analiz yapmam gerekiyor iste hangi gen ne kadar expre olmus zarttikzorttik seyler mesela dunki 90 milyon okumali bi ornekmis makalede de 12 ornek var 90×12 bir de cift sira okuma var 90×12×2 biraz zorlar bizi dedi hoca da smdi yeni makale bakiom
October 23, 2026 at 6:19 AM
Makalede kullanilan rnaseq verilerini kendi pc indirip analiz yapmam gerekiyor iste hangi gen ne kadar expre olmus zarttikzorttik seyler mesela dunki 90 milyon okumali bi ornekmis makalede de 12 ornek var 90×12 bir de cift sira okuma var 90×12×2 biraz zorlar bizi dedi hoca da smdi yeni makale bakiom
12/
Keep it simple:
Internal/
├── RNAseq/
├── WGS/
Public/
├── TCGA/
├── ENCODE/
Each with a README. Just say what the data is and where it came from.
Keep it simple:
Internal/
├── RNAseq/
├── WGS/
Public/
├── TCGA/
├── ENCODE/
Each with a README. Just say what the data is and where it came from.
October 24, 2026 at 1:15 PM
12/
Keep it simple:
Internal/
├── RNAseq/
├── WGS/
Public/
├── TCGA/
├── ENCODE/
Each with a README. Just say what the data is and where it came from.
Keep it simple:
Internal/
├── RNAseq/
├── WGS/
Public/
├── TCGA/
├── ENCODE/
Each with a README. Just say what the data is and where it came from.
Help!
I remember reading a very good opinion paper about "qRT-PCR vs RNAseq" and why it doesn't make sense to "validate" RNAseq data that way.
Does that paper ring a bell to anyone?
I remember reading a very good opinion paper about "qRT-PCR vs RNAseq" and why it doesn't make sense to "validate" RNAseq data that way.
Does that paper ring a bell to anyone?
October 20, 2026 at 11:08 AM
Help!
I remember reading a very good opinion paper about "qRT-PCR vs RNAseq" and why it doesn't make sense to "validate" RNAseq data that way.
Does that paper ring a bell to anyone?
I remember reading a very good opinion paper about "qRT-PCR vs RNAseq" and why it doesn't make sense to "validate" RNAseq data that way.
Does that paper ring a bell to anyone?
#gComm
resolveS infers RNA-seq library strandedness genome-independently using universal rRNA alignments, classifying 1,091 benchmark libraries within seconds under 0.5 GiB memory.
Details: https://www.maxapress.com/article/doi/10.48130/gcomm-0026-0020
#RNAseq #Bioinformatics #QualityControl
resolveS infers RNA-seq library strandedness genome-independently using universal rRNA alignments, classifying 1,091 benchmark libraries within seconds under 0.5 GiB memory.
Details: https://www.maxapress.com/article/doi/10.48130/gcomm-0026-0020
#RNAseq #Bioinformatics #QualityControl
October 23, 2026 at 3:26 AM
#gComm
resolveS infers RNA-seq library strandedness genome-independently using universal rRNA alignments, classifying 1,091 benchmark libraries within seconds under 0.5 GiB memory.
Details: https://www.maxapress.com/article/doi/10.48130/gcomm-0026-0020
#RNAseq #Bioinformatics #QualityControl
resolveS infers RNA-seq library strandedness genome-independently using universal rRNA alignments, classifying 1,091 benchmark libraries within seconds under 0.5 GiB memory.
Details: https://www.maxapress.com/article/doi/10.48130/gcomm-0026-0020
#RNAseq #Bioinformatics #QualityControl
Human aorta is a mm-thick 50-layered organ
#SmoothMuscleCell phenotypic gradients across aortic media?👇
Here is an important study from Dr. Hiromi Yanagisawa
Micro-biopsies RNAseq from 4 distinct layers in 👤aortic media
5 BAV + 4 Sporadic
#AortaEd
#JVSVS 2026
jvsvs.org/article/S266...
#SmoothMuscleCell phenotypic gradients across aortic media?👇
Here is an important study from Dr. Hiromi Yanagisawa
Micro-biopsies RNAseq from 4 distinct layers in 👤aortic media
5 BAV + 4 Sporadic
#AortaEd
#JVSVS 2026
jvsvs.org/article/S266...
October 23, 2026 at 6:54 PM
Human aorta is a mm-thick 50-layered organ
#SmoothMuscleCell phenotypic gradients across aortic media?👇
Here is an important study from Dr. Hiromi Yanagisawa
Micro-biopsies RNAseq from 4 distinct layers in 👤aortic media
5 BAV + 4 Sporadic
#AortaEd
#JVSVS 2026
jvsvs.org/article/S266...
#SmoothMuscleCell phenotypic gradients across aortic media?👇
Here is an important study from Dr. Hiromi Yanagisawa
Micro-biopsies RNAseq from 4 distinct layers in 👤aortic media
5 BAV + 4 Sporadic
#AortaEd
#JVSVS 2026
jvsvs.org/article/S266...
To address we this, we (with @omrykoren.bsky.social and Amir Erez) decided to develop a tool, CompoRes. You can feed this tool multidimensional data (RNAseq, metabolomics, etc.) together with microbial compositional data (metagenomics, 16S, etc.) and it will tell you the likelihood that /4
Address Me
ALT: Address Me
static.klipy.com
October 19, 2026 at 5:32 PM
To address we this, we (with @omrykoren.bsky.social and Amir Erez) decided to develop a tool, CompoRes. You can feed this tool multidimensional data (RNAseq, metabolomics, etc.) together with microbial compositional data (metagenomics, 16S, etc.) and it will tell you the likelihood that /4
1. We found that differential growth that drives upward leaf movement seems powered by regulation in the abaxial petiole cortex cells. We were able to distinguish these in the scRNAseq data using bulk RNAseq markers from longitudinally dissected petioles, done by @lisaoskam.bsky.social
October 18, 2026 at 8:35 PM
1. We found that differential growth that drives upward leaf movement seems powered by regulation in the abaxial petiole cortex cells. We were able to distinguish these in the scRNAseq data using bulk RNAseq markers from longitudinally dissected petioles, done by @lisaoskam.bsky.social
1- Single-cell RNAseq identifies MGAT1-MGAT5 branched pathway as a feature that regulates IL-17A-producing γδ T cells.
2- Loss of branched N-glycans promotes a pro-inflammatory, IL-17A-producing γδ T cell phenotype and exacerbates psoriasis disease in experimental models.
2- Loss of branched N-glycans promotes a pro-inflammatory, IL-17A-producing γδ T cell phenotype and exacerbates psoriasis disease in experimental models.
October 17, 2026 at 5:40 PM
1- Single-cell RNAseq identifies MGAT1-MGAT5 branched pathway as a feature that regulates IL-17A-producing γδ T cells.
2- Loss of branched N-glycans promotes a pro-inflammatory, IL-17A-producing γδ T cell phenotype and exacerbates psoriasis disease in experimental models.
2- Loss of branched N-glycans promotes a pro-inflammatory, IL-17A-producing γδ T cell phenotype and exacerbates psoriasis disease in experimental models.
@veupathdb.org's new differential exp search shows results on an interactive volcano plot 🌋
You can weigh fold change AND significance together, then set thresholds and pull out your gene list in a click.
Click on a DE button to try:
veupathdb.org/veupathdb/ap...
#data #RNAseq #Bioinformatics
You can weigh fold change AND significance together, then set thresholds and pull out your gene list in a click.
Click on a DE button to try:
veupathdb.org/veupathdb/ap...
#data #RNAseq #Bioinformatics
October 15, 2026 at 2:49 PM
@veupathdb.org's new differential exp search shows results on an interactive volcano plot 🌋
You can weigh fold change AND significance together, then set thresholds and pull out your gene list in a click.
Click on a DE button to try:
veupathdb.org/veupathdb/ap...
#data #RNAseq #Bioinformatics
You can weigh fold change AND significance together, then set thresholds and pull out your gene list in a click.
Click on a DE button to try:
veupathdb.org/veupathdb/ap...
#data #RNAseq #Bioinformatics
Really cool paper that uses single-cell RNA-seq in evolutionary genomics & popgen to enhance our understanding of gene function in nonmodel organisms, where gene ontology analyses with distantly related species often fall short.
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
Rates of Evolution Differ Between Cell Types Identified by Single‐Cell <fc>RNAseq</fc> in Threespine Stickleback
Rates of evolutionary change vary by gene. While some broad gene categories are highly conserved with little divergence over time, others undergo continuous selection pressure and are highly divergen...
onlinelibrary.wiley.com
October 16, 2026 at 1:56 PM
Really cool paper that uses single-cell RNA-seq in evolutionary genomics & popgen to enhance our understanding of gene function in nonmodel organisms, where gene ontology analyses with distantly related species often fall short.
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
🧬 How does ageing with frailty reshape immune responses?
This open‑access study links altered neutrophil signalling to impaired chemotaxis and increased ROS/NET production, highlighting key features of inflammageing.
👉 vist.ly/5nnmh
#ImmuneAgeing26
This open‑access study links altered neutrophil signalling to impaired chemotaxis and increased ROS/NET production, highlighting key features of inflammageing.
👉 vist.ly/5nnmh
#ImmuneAgeing26
Neutrophil Functional Analysis in Frailty and Health
In this study we have combined RNAseq with functional experiments to describe the phenotype of neutrophils from people with frailty. We found that frailty
doi.org
October 16, 2026 at 10:59 AM
🧬 How does ageing with frailty reshape immune responses?
This open‑access study links altered neutrophil signalling to impaired chemotaxis and increased ROS/NET production, highlighting key features of inflammageing.
👉 vist.ly/5nnmh
#ImmuneAgeing26
This open‑access study links altered neutrophil signalling to impaired chemotaxis and increased ROS/NET production, highlighting key features of inflammageing.
👉 vist.ly/5nnmh
#ImmuneAgeing26
⚒️ Pipeline Composition: any typed pipeline is now a callable workflow. Chain pipelines like fetchngs → rnaseq in a single run, with downstream work starting as upstream results arrive.
October 15, 2026 at 9:58 AM
⚒️ Pipeline Composition: any typed pipeline is now a callable workflow. Chain pipelines like fetchngs → rnaseq in a single run, with downstream work starting as upstream results arrive.
Long reads need long cDNA. New long-read RNA-seq data with UltraMarathonRT® at the #ASHG2026 poster session, Wed Oct. 21, 2:30–4:30 PM EDT, then Booth #1722.
Learn more: bit.ly/4i68N0v
#UltraMarathonRT #RNASky #RNASeq #ASHG26
Learn more: bit.ly/4i68N0v
#UltraMarathonRT #RNASky #RNASeq #ASHG26
October 15, 2026 at 4:18 PM
Long reads need long cDNA. New long-read RNA-seq data with UltraMarathonRT® at the #ASHG2026 poster session, Wed Oct. 21, 2:30–4:30 PM EDT, then Booth #1722.
Learn more: bit.ly/4i68N0v
#UltraMarathonRT #RNASky #RNASeq #ASHG26
Learn more: bit.ly/4i68N0v
#UltraMarathonRT #RNASky #RNASeq #ASHG26
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
New on @veupathdb.org! Differential expression analysis in your browser, no coding required. 🧬
Explore differential expression data using PCA & volcano plots and generate gene lists for further analysis.
TRY IT! Click on a DE button-
veupathdb.org/veupathdb/ap...
#RNAseq #data #bioinformatics
Explore differential expression data using PCA & volcano plots and generate gene lists for further analysis.
TRY IT! Click on a DE button-
veupathdb.org/veupathdb/ap...
#RNAseq #data #bioinformatics
October 13, 2026 at 6:33 PM
New on @veupathdb.org! Differential expression analysis in your browser, no coding required. 🧬
Explore differential expression data using PCA & volcano plots and generate gene lists for further analysis.
TRY IT! Click on a DE button-
veupathdb.org/veupathdb/ap...
#RNAseq #data #bioinformatics
Explore differential expression data using PCA & volcano plots and generate gene lists for further analysis.
TRY IT! Click on a DE button-
veupathdb.org/veupathdb/ap...
#RNAseq #data #bioinformatics
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
Before you trust a gene list, look at your samples. 👀
Increase your confidence in your results by examining the experimental samples using PCA, built into VEuPathDB's new differential expression search.
Click on a DE button to try it for yourself-
veupathdb.org/veupathdb/ap...
#RNAseq #data
Increase your confidence in your results by examining the experimental samples using PCA, built into VEuPathDB's new differential expression search.
Click on a DE button to try it for yourself-
veupathdb.org/veupathdb/ap...
#RNAseq #data
October 14, 2026 at 2:16 PM
Before you trust a gene list, look at your samples. 👀
Increase your confidence in your results by examining the experimental samples using PCA, built into VEuPathDB's new differential expression search.
Click on a DE button to try it for yourself-
veupathdb.org/veupathdb/ap...
#RNAseq #data
Increase your confidence in your results by examining the experimental samples using PCA, built into VEuPathDB's new differential expression search.
Click on a DE button to try it for yourself-
veupathdb.org/veupathdb/ap...
#RNAseq #data
Interested in learning how to analyse RNA-seq data with R and Bioconductor?
Our online course, Introduction to RNA Sequencing Data Analysis with R/ @bioconductor.bsky.social will take place on 2,3,5,6,9,10 November.
#RNAseq @bioconductor.bsky.social
www.physalia-courses.org/courses-work...
Our online course, Introduction to RNA Sequencing Data Analysis with R/ @bioconductor.bsky.social will take place on 2,3,5,6,9,10 November.
#RNAseq @bioconductor.bsky.social
www.physalia-courses.org/courses-work...
Introduction to RNA sequencing data analysis with R/Bioconductor
9, 11, 13, 16, 17, 18 November 2026 To foster international participation, this course will be held online
www.physalia-courses.org
October 14, 2026 at 12:06 PM
Interested in learning how to analyse RNA-seq data with R and Bioconductor?
Our online course, Introduction to RNA Sequencing Data Analysis with R/ @bioconductor.bsky.social will take place on 2,3,5,6,9,10 November.
#RNAseq @bioconductor.bsky.social
www.physalia-courses.org/courses-work...
Our online course, Introduction to RNA Sequencing Data Analysis with R/ @bioconductor.bsky.social will take place on 2,3,5,6,9,10 November.
#RNAseq @bioconductor.bsky.social
www.physalia-courses.org/courses-work...