Tag: RNAseq

Job DescriptionThis is a Pre-Fellowship for early career researchers wanting to establish a career in MND translational research and become MND research leaders of the future. The postholder will have a leading role in an exciting new project funded by Motor Neurone Disease Association and MND Scotland. The project is…

dc.contributor.author Lim, Ryan G dc.contributor.author Al-Dalahmah, Osama dc.contributor.author Wu, Jie dc.contributor.author Gold, Maxwell P dc.contributor.author Reidling, Jack C dc.contributor.author Tang, Guomei dc.contributor.author Adam, Miriam dc.contributor.author Dansu, David K dc.contributor.author Park, Hye-Jin dc.contributor.author Casaccia, Patrizia dc.contributor.author Miramontes, Ricardo dc.contributor.author Reyes-Ortiz, Andrea M dc.contributor.author Lau, Alice dc.contributor.author Hickman, Richard A dc.contributor.author Khan,…

Starting from a list of gene IDs with optional expression values Starting from a single count table (RNAseq) or intensity table (microarray) Starting with several gene expression tables for meta-analysis Uploading raw RNAseq files (any species) for mapping & quantification Starting with a network file (sif, graphml, json) News &…

I am trying to trim paired end reads using Trim-Galore. I have made sure that the files match based on the total reads processed in the output txt file from trim-galore. One of the files trimmed correctly but when I try some of the others the total written and quality…

We are seeking a talented, highly motivated Senior Bioinformatics Research Scientist to lead our bioinformatics pipeline and develop innovative solutions for analyzing and visualizing omics data related to innate immune signaling projects. The candidate will work both collaboratively and independently on projects within the Kanneganti lab in the Department of…

Problem with DRAGEN RNAseq hashtable directory 1 Dear all, Recently I wrote a code to work with DRAGEN and RNAseq pipeline. I use this command: /opt/edico/bin/dragen -f -l \ -r refdir \ -1 ${forward} \ -2 ${reverse} \ -a ${gtf} \ –output-dir output/${sample} \ –output-file-prefix ${sample} \ –RGID ${sample}_group_id \…

Quantile normalisation on RNAseq with substantial differences on sample size 0 I tried vst and rlog from DESEq2 for my RNA seq data. But i suspect the largest group (condition 1 with 60 samples) has affected the variance from other groups (condition2 with 20 samples, condition 3 and 4 with…

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma, a cancer that starts in cells called lymphocytes, which are part of the body’s immune system. Its progression and prognosis vary significantly among patients, making it crucial to identify prognostic factors that can help predict patient outcomes…

EPFL, the Swiss Federal Institute of Technology in Lausanne, is one of the most dynamic university campuses in Europe and ranks among the top 20 universities worldwide. The EPFL employs more than 6,500 people supporting the three main missions of the institution: education, research and innovation. The EPFL campus offers…

Anavex Life Sciences Corp. (“Anavex” or the “Company”) (Nasdaq: AVXL), a clinical-stage biopharmaceutical company developing differentiated therapeutics for the treatment of neurodegenerative and neurodevelopmental disorders including Alzheimer’s disease, Parkinson’s disease, Rett syndrome and other central nervous system (CNS) diseases, today announced the first entire clinical gene pathway data from the…

Key Points Question  What is the association of PIK3CA mutations, response to therapy, and outcome by hormone receptor (HR) status and intrinsic subtype among patients with ERBB2/HER2-positive early breast cancer (EBC) treated in a clinical trial? Findings  In this cohort study of 184 patients enrolled in the phase 3 trial…

Job Description Who we are Genomines is a young biotechnology company based in Paris and Saclay, specialized in sustainable extraction of Nickel from plants. The mission of Genomines is to usher in a new era of sustainable mining by using genetically enhanced plants to extract metals from soil (agromining). Through…

Since the idea of genetic regulation was first postulated back in the 1950s, our scientific understanding of the transcriptome has deepened greatly.1 Looking into the transcriptome of cells and tissues has helped scientists to understand the biological processes that drive both health and disease; however, the complex and occasionally mysterious…

CRISPR/Cas9-induced homozygous knockout of nexn causes progressive cardiac dysfunction without affecting skeletal muscle function in zebrafish Several studies in different animal models and cardiomyopathy patients have shown that loss of NEXN is leading to DCM which is characterized by an impaired contractility of the heart6,10,12. Homozygous loss of NEXN mostly…

Repurposing amiodarone as a targeted SIRT3 activator that induces autophagic/mitophagic cell death in acute myelocytic leukemia (RNAseq), this is the RNAseq raw data of this article, and there are three duplicate samples. CK represents control group, T represents adminstration group. Funding Science and Technology Project of Haihe Laboratory of Modern…

I am working with data from an RNAseq containing expression values for about 3000 genes, including measurements from diseased and control patients. My goal is to train machine learning models, Lasso and random forest, in order to select which subset of genes is able to perform better disease prediction. I…

Title: Bioinformatics Scientist Location: Cambridge, MA 02141 Duration: 12 Months Pay rate starts from $70/hr. Note: * Shift: M-F(9am-6pm)EST * Work location: Cambridge, MA-Hybrid (2 days/week) or Remote (ideally, eastern time zone) Qualifications: Education Minimum Requirement: * Ph.D. (or 5+ years of relevant experience) in Bioinformatics, Biostatistics, Computational…

Allam RM, Al-Abd AM, Khedr A, Sharaf OA, Nofal SM, Khalifa AE, Mosli HA, Abdel-Naim AB (2018) Fingolimod interrupts the cross talk between estrogen metabolism and sphingolipid metabolism within prostate cancer cells. Toxicol Lett 291:77–85 Article  CAS  PubMed  Google Scholar  Andrews S et al (2010) FastQC: a quality control tool…

News:NGS Data Analysis Workshops 2024 0 Exciting News: ecSeq Bioinformatics 2024 Workshops Are Here! We’re thrilled to announce our diverse range of bioinformatics workshops for 2024, now open for registration! Whether you’re a beginner or looking to deepen your expertise, our courses are designed to elevate your skills in the…

downstream analysis on the output of nf-core/rnaseq pipeline 1 Hello everyone, I ran nf-core/rnaseq pipeline successfully, now I want to do downstream analysis like machine learning on the generated output files from this pipeline. Should I use salmon.merged.gene_counts.tsv for that and apply log transformation to normalize it before doing downstream…

Greetings to my fellow researchers! As we delve into the ever-evolving landscape of genomics, one frontier that has truly revolutionized our understanding of cellular heterogeneity is Single Cell RNA Sequencing (scRNASeq). In my quest for proficiency in this transformative field, I embarked on a fascinating journey exploring various scRNASeq analysis…

Abstract Muscle regeneration is associated with transient induction of cellular senescence. However, the role of senescence in muscle regeneration of young mice remains unclear. Using a mouse model deficient in both Cdkn1a and Cdkn2a, we find that a marked reduction in senescent cells correlates with delayed muscle regeneration. Single-cell RNA…

Hi all, I’ve come back to WGCNA after some years and have run into a bit of a quirky result when looking at my soft power thresholds depending correlation the methods I use. Generally, this topic has been discussed a fair bit – but was looking to see if anyone…

Título:  Autor:  Garrigós, Marta; Ylla, Guillem CSIC ORCID; Martínez de la Puente, Josué CSIC ORCID; Figuerola, Jordi CSIC ORCID ; Ruiz-López, María José CSIC ORCID Palabras clave:  TranscriptomesAvian malariaCulexGene expresion Fecha de publicación:  12-dic-2023 Editor:  DIGITAL.CSIC Citación:  Garrigós, Marta; Ylla, Guillem; Martínez de la Puente, Josué; Figuerola, Jordi; Ruiz-López, María…

Using STAR’s readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport 1 @e0db819c Last seen 1 day ago United States Hi, I am new to RNA-seq analysis. I have finished RNA alignment using STAR, and got ReadsPerGene.out.tab outputs. I am trying to use tximport to build a gene-level…

Linear Model Fitting and Colinearity 1 @7220be07 Last seen 9 hours ago United States Hello All, I have an RNAseq experiment with paired samples (before and after treatment). For each sample, I also have metadata on the patient such as sex. The only comparison that I care about is the…

Abstract Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced…

What are the advantages and disadvantages of RNA-seq compared to other methods for studying gene expression?5 answersRNA-seq has several advantages over other methods for studying gene expression. Firstly, RNA-seq can detect new transcripts and coding regions, which is not possible with microarray technology. Secondly, RNA-seq provides less noisy data compared…

Transcribed image text: Answer questions 37-39 based on the options (A, B, C, or D) below. Each graph represents the RNAseq (top) and Ribo-seq (bottom) reads aligned to a reference gene. 37) Which graph represents the mRNA that is generating more protein? 38) Which graph represents an mRNA without introns?…

Bowtie2 end-to-end versus local alignment for small RNAseq 0 hello, I’m working with small RNAseq data from Illumina Trueseq small RNA, my reads have been trimmed and when I align with bowtie2’s –end-to-end alignment, I get 96% overall alignment. When I use bowtie2’s –local alignment I get only 30% alignment….

ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…

Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder 0 Hi all, I am running a workflow to identify single copy orthogroups from RNAseq data including 9 species in a family of non-model organisms. All 9 species are closely related enough that they can be aligned to…

Java class error message when using BBDuk 0 I am trying to run BBDuk to quality trim and filter my illumina whole genome sequences. I have used other trimming scripts before and have not had a problem. Although this is my first time preprocessing sequencing data from Quantseq samples. I…

Normalization of RNA captureSeq data (<20 genes captured) 0 Hi all Hope someone can help with this. We are working on RNA captureSeq experiments where we perform targeted RNAseq on 20 genes of interest (+ probes for the 92 ERCC standards). In the initial phase of the experiment we were…

News:University of Connecticut Single Cell RNA-seq Workshop December 12-15, 2023 0 Join UConn’s Computational Biology Core for a Single Cell RNAseq Workshop December 12-15, 2023 Scope of the workshop: Introduction to different data file formats. Understanding the Considerations while designing single-cell RNA-seq experiments, Hands on steps to convert raw single-cell…

Hello everyone, I am stuck trying to analyze some single-end RNAseq data from human tissue. My issue is that the alignment with HISAT 2 went very well: 94.95% overall alignment rate. However, when I use featureCounts, I get: 5.7% when I set the strandSpecific parameter to 1. 5.3% when I…

Curated model organism gene functional annotations 0 Hi, I’m working with a model organism for the first time – C. elegans nematodes – and have created a list of differential expressed genes from some RNAseq data the lab had. One of the things I like to do is look for…

How can transfer learning be used to cluster single-cell RNA-seq data across species and batch?5 answersTransfer learning can be used to cluster single-cell RNA-seq data across species and batch. SATURN is a deep learning method that learns universal cell embeddings by encoding genes’ biological properties using protein language models. By…

Dr. Noam Auslander and authors trained a neural network to identify cancer risk from microbes Philadelphia, PA, Dec. 06, 2023 (GLOBE NEWSWIRE) — Wistar scientists have developed a new tool that can help identify cancer-associated microbes by using machine learning technology. Under the leadership of Dr. Noam Auslander — assistant professor…

Company Summary: Each day, the lives of more than 2 billion people across the globe are impacted by chronic diseases. Moreover, the economic burden on society of treating chronic disease is spinning out of control. Today, this dire situation appears unlikely to change as >95% of global healthcare costs are…

DOI: 10.18129/B9.bioc.DropletUtils     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DropletUtils. Utilities for Handling Single-Cell Droplet Data Bioconductor version: 3.15 Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data…

RNASeq time course analysis, missing time points for control 1 @f0fee368 Last seen 1 minute ago United Kingdom Hi there, I am currently doing a project for my masters degree on some pre-existing time course RNASeq data of covid progression in a cell line of caco-2. I have time points…

The global Whole Exome Sequencing Market was valued at USD 1.4 Billion in 2022 and it is anticipated to grow up to USD 7.4 Billion by 2032, at a CAGR of 18.1% during the forecast period. Request free sample copy of this research study: www.globalinsightservices.com/request-sample/GIS10515/?utm_source=pranalipawar&utm_medium=Openpr&utm_campaign=04122023 Exome sequencing is a method…

gme December 1, 2023, 4:02pm 1 Hi, I followed the scanpy tutorial to integrate scRNAseq clusters on spatial RNAseq samples. Now I am trying to measure the colocalization and the distances between these clusters on the spatial samples. I tried to use squidpy interaction_matrix or nhood_enrichment but it does not…

Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…

R3 VAR14 vs RBC no TNF k-means q0.05 1. Genelist Selection groupsName<-“R3_VAR14_kmeans_q0.05” countsTable<-read.delim(“RNAseq2019July_5.txt”, header = TRUE, sep = “\t”,check.names=FALSE,row.names=1) head(countsTable) AllGeneNames<-countsTable$Gene_Symbol #head(AllGeneNames) tempA<-countsTable topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_0h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_0h))####find indexes listA<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_2h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_2h))####find indexes listB<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_6h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_6h))####find indexes listC<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_20h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_20h))####find indexes listD<-tempA[ topDEgenes,…

From TPM to raw counts 0 I am deconvoluting a bulk RNASeq experiment using scRNA to generate a signature of cell types using CIBERSORTX. The program asks you bulk data normalized, so I used TPM. The finction ‘high resolution’ returns normalized expressione (I presume) per cell type. To perform differential…

Transcribed image text: A scientist collects RNAseq data examining expression differences in the peripheral blood from individuals taking medication to treat migraines caused by hormone replacement therapy. Group A is a cohort or similar people taking a placebo without migraine medicine and Group B is a cohort of similar people…

Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom 0 Hi everyone, first of all, I’m new for bioinformatics. I have downloaded RNAseq data of TCGA-LUAD from UCSC that had already normalized RSEM normalized count and log2 transformed (log2 normcount+1). i wonder if i can…

What is single cell?5 answersSingle cell refers to the analysis of individual cells at a high-resolution level, allowing for a deeper understanding of cellular behavior and mechanisms. It overcomes the challenge of cellular heterogeneity and provides new methods for studying the relationship between individual cells and the body. Single cell…

Plant biostimulants have been earmarked as one of the major groups of new plant growth promoting substances to drive a much-needed revolution in agriculture. One such PB, BC204, has been used to great success, but there is no peer-reviewed data to explain the possible mechanisms by which it exerts its…

ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…

BC204 is a citrus-based plant extract applied as a plant biostimulant on a variety of plant species in South Africa, China and Australia. Although there are reports that it elicits physiological responses such as an increase in crop yield and fruit quality, no molecular data is available to explain the…

Salmon indices differences 1 I am trying to run Salmon locally on prostate cancer samples, and I used this command: salmon quant -i data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_sa_index/default -l A -1 SRR21898893_1.fastq.gz -2 SRR21898893_2.fastq.gz –validateMappings –gcBias -o transcripts_quant I downloaded the pre-built versions of the partial decoy (salmon_partial_sa_index) and full decoy (salmon_sa_index) indices from…

What type of cancer did they study in this paper? 1 I am currently reviewing a research paper which focuses on investigating the effects of anti-PD1 drugs in cancer patients, utilizing single-cell RNA sequencing on T-cells. The authors have detailed the process of collecting blood samples, yet they have not…

Gustafsson C, Hauenstein J, Frengen N, Krstic A, Luc S, Månsson R BMC Genomics 24 (1) 205 [2023-04-17; online 2023-04-17] RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts…

Viral genes not showing up in combined mouse+virus alignment 1 I created a combined MHV-A59 and mm10 fasta and GTF file using the linux cat command. The last two entries of the mm10 and first two of the A59 of the combined GTF looks like this: I then made a…

In recent decades, the development of computational and bioinformatics tools and websites for life sciences has increased exponentially. This great development has gone hand in hand with the availability of genome, proteome and macromolecule structure databases, and also of functional experiments, including microarray and RNAseq expression data, RNA-protein interactions, ChIP-seq,…

Using ggplot2 to make barplots of RNASeq data – maintaining sample metadata when pivoting from wide to long format 0 I am currently trying to replicate the following plots of my RNASeq data made by the program Biolayout using ggplot2. This is a network analysis tool which clusters together genes…

Generate Read counts from bam file 2 Currently i am working on a project related to LHON disease (rare mitochondrial disorder which leads to progressive visual loss). I have 9 RNA-seq fastq files out of which 3 are for carriers, 3 for affected and 3 for control. Data downloaded is…

Precision oncology approaches have made great strides harnessing individual tumor mutation profiles to guide targeted therapy choices. However, deeper molecular insights are needed to improve personalized treatment decisions that are tailored to specific molecular characteristics of a tumor. Integrating gene expression analysis in personalized oncology provides an additional level of…

CPTAC data, download, merge 1 Hey friends I downloaded RNA seq data of CPTAC from GDC portal. I want to merge them as one file. I have my python script and manifest file in the same folder and I am running the following code in the command prompt to merge…

Running STAR on fastq file generated from a RNA-seq experiment 1 Hi, I am new to bioinformatics, especially on the command line. I am trying to run STAR alignment on pairs of fastq.gz files from several samples generated as part of an RNAseq experiment. My goal is to perform splice…

DEseq2 input 1 Hello Guys, @Michael Love I have a transcriptomics dataset and did rnaseq/nf-core pipeline by salmon-star. my output of the salmon-star folder is as follows: salmon.merged.gene_counts.tsv salmon.merged.gene_counts_length_scaled.tsv salmon.merged.gene_counts_scaled.tsv salmon.merged.gene_lengths.tsv salmon.merged.gene_tpm.tsv salmon.merged.transcript_counts.tsv salmon.merged.transcript_lengths.tsv salmon.merged.transcript_tpm.tsv tx2gene.tsv my question is: which one of these files should be an input for Deseq2…

Combine Geoids 0 I have the following geo IDs: GSE230470—>Calorie Restriction Outperforms Bariatric Surgery in Reversing Obesity-Driven Tumor Progression in a Mouse Model of Triple Negative Breast Cancer-Study1_tumor GSE230471—>Calorie Restriction Outperforms Bariatric Surgery in Reversing Obesity-Driven Tumor Progression in a Mouse Model of Triple Negative Breast Cancer-Study2_tumor GSE174761—>Bariatric surgery reduces…

Open access•Posted Content•DOI 05 Oct 2022 The paper provides a protocol for single nucleus RNA sequencing (snRNAseq) from frozen skeletal muscle, but it does not explicitly provide the detailed steps of the protocol. Open access•Journal Article•DOI The provided paper does not provide information on how to write a protocol for…

Rv3907c is the CCA-adding enzyme in Mycobacterium It remains unclear whether the rv3907c gene product, originally annotated as poly(A) polymerase, is in fact the CCA-adding enzyme in Mtb. Rv3907c is composed of three domains, an N-terminal class II polymerase β superfamily domain, a central RNA-binding domain and a C-terminal HD…

Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes 0 @4b83ad99 Last seen 1 day ago Canada Hello, This question is crossposted from Biostars as I wasn’t sure which platform is the more appropriate one for asking it. I am studying the gene expression of a…

DOI: 10.18129/B9.bioc.gDNAx   Diagnostics for assessing genomic DNA contamination in RNA-seq data Bioconductor version: Release (3.18) Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and,…

Genome sequencing and assembly of R. tetraphylla After DNA extraction from young leaves and sequencing, the R. tetraphylla genome was first assembled into 1008 contigs with an N50 of 3.7 Mb. After haplotigs removal and a final pilon polishing, the 364,945,498 bp final assembly was distributed across 76 scaffolds with an N50…

Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset 0 Hello all, I have some feature matrixes from a bulk RNA seq analysis pipeline, and I want to perform bulk deconvolution to get relative single cell proportions. Some of the samples are from WT mice, while others are from…

A new analysis sheds light on the molecular processes that occur when a carnivorous species of fungus known as Arthrobotrys oligospora detects, traps and ingests a worm. The a. oligospora’ usually obtains its nutrients from decaying organic matter, but hunger and the presence of nearby worms prompts it to build…

Selecting suitable geoid for study 0 I am working on the study “Phytosterols’ Effect on Epigenetic Mechanisms in Breast Cancer.” For this purpose, I have to select geoids. My basic purpose is to select an RNA-seq experiment. I searched the following geoids: GSE230470—>Calorie Restriction Outperforms Bariatric Surgery in Reversing Obesity-Driven…

Mitochondrial genes in single cell nuclear RNAseq data 2 I have done several single cell nuclear RNAseq experiments on human brain tissue. I followed this protocol outlined in Krishnaswami et al www.ncbi.nlm.nih.gov/pmc/articles/PMC4941947/. The percentage of viable (intact) cells out of the total nuclei suspension is less than 5% – and…

Salmon index problem 0 Hello, I’m trying to use Salmon in the mapping-based mode, and I downloaded the full decoy salmon indices via refgenie list here using the refgenie command refgenie pull hg38/salmon_sa_index and it download the full folder locally. Now I have this index folder and SRR21898893_1.fastq.gz and SRR21898893_2.fastq.gz…

Hi, Im exploring and integrating the LUAD TGCA transcriptomic and genomic data. Im trying to do so both with TCGAbiolinks in R and cBioportal. With TCGAbiolinks I acces the data this way (bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html#TCGAvisualize:_Visualize_results_from_analysis_functions_with_TCGA%E2%80%99s_data) query <- GDCquery(#legacy = T, project = “TCGA-LUAD”, data.category = “Transcriptome Profiling”, data.type = “Gene Expression Quantification”,…

I have an RNAseq dataset that I want to perform differential gene-expression analysis on. The dataset consists of 3 groups = macrophages deriving from adults (n=6), term-born infants (n=5), and preterm infants (n=3). Each sample has been treated with an immune-stimulus, or left untreated (paired samples). Group Treatment Sample_Nr Sample_within_group…

image:  Glowing traps. view more  Credit: Hung-Che Lin (CC-BY 4.0, creativecommons.org/licenses/by/4.0/) A new analysis sheds light on the molecular processes involved when a carnivorous species of fungus known as Arthrobotrys oligospora senses, traps and consumes a worm. Hung-Che Lin of Academia Sinica in Taipei, Taiwan, and colleagues present these findings…

DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample 1 @e3bc7671 Last seen 54 minutes ago United Kingdom Hello, This is a question related to RNAseq expression and the need to extract biologically relevant results at single patient level. For context,…

Hello all, Background: I’ve inherited a new RNAseq data set and am thinking about updating my approaches (last time I did this I was using HISAT and Cuffdiff). I’d like some opinions on best strategies to disentangle/filter out parasite microbe reads from infected host reads before preforming a differential gene…

Interpretation of mean-variance trend in voom 0 Dear biostars-community! I am still very new to the field of RNAseq analysis and I struggle with interpretation of the mean-variance trend. Specifically, I am not sure whether I can continue with the analysis based on my “voom plot” (see below). Can anyone…

Genome annotation (proving evidance from the RNA-seq raw reads) 0 Dear All, I have this question but need help answering it using the technical process (From mapping to quantification). I recently annotated a genome of eukaryotic species. So, After combining three methods using EvidanceModeler. The annotation of protein-coding genes yielded…

. 2023 Nov 17:12:RP89338. doi: 10.7554/eLife.89338. Affiliations Expand Affiliation 1 Vollum Institute, Oregon Health & Science University, Portland, United States. Item in Clipboard Jimmy J Kelly et al. Elife. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 Nov 17:12:RP89338. doi: 10.7554/eLife.89338. Affiliation 1 Vollum Institute, Oregon Health &…

Using single cell multi-omics analysis to predict treatment outcome, develop disease prognostics and track patient responses to CAR T therapies COLOGNE, Germany, Nov. 17, 2023 /PRNewswire/ — Singleron Biotechnologies, a company at the forefront of developing and commercializing innovative single cell multi-omic analysis solutions for precision medicine, has announced two…

Hi, I am getting error while running HTseq. This is the command and the error: htseq-count -q -f bam -s yes Ac1_mapped/ac1_mappedAligned.bam /global/home/users/catalinacastro/star/genome/genomic_v2.gtf count.txt Error occurred when processing GFF file (line 637338 of file /global/home/users/catalinacastro/star/genome/genomic_v2.gtf): not enough values to unpack (expected 9, got 1) [Exception type: ValueError, raised in init.py:221]…

how to fix low RNA input in bulk RNAseq data analysis? 0 I have some RNAseq data and when I got count data, I checked the expression of some house keeping genes and in few samples I saw they are up to 10 fold less than other samples showing that…

Error with HTseq RNAseq read count 0 Hi, I am getting error while running HTseq. This is the command and the error: htseq-count -q -f bam -s yes Ac1_mapped/ac1_mappedAligned.bam /global/home/users/catalinacastro/star/genome/genomic_v2.gtf count.txt Error occurred when processing GFF file (line 637338 of file /global/home/users/catalinacastro/star/genome/genomic_v2.gtf): not enough values to unpack (expected 9, got…

Can FPKM be used to create bar graphs for DEGs? 0 Hi, I have an Excel sheet of RNAseq results. The raw data was analyzed by a company and was not available to me. I have three sets of data on this sheet besides the gene names and p-values: Raw…

DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment 0 @724e8e11 Last seen 3 hours ago Australia Hi everyone, first time poster. I have resorted to this because I can’t seem to find substantive answers to my question (or don’t exactly fit my question), nor…

Mapping Mouse RNAseq Marker Genes to Reactome Pathways 0 Hello, In my project, I need to correlate single-cell RNAseq marker genes (after clustering) with specific pathways, for example metabolism and the immune system in Mus musculus. While I have found resources for Homo sapiens, I’m struggling to locate equivalent data…

Doubt about RNASeq Paired-end process 0 Hi, I have a doubt regarding how an RNASeq experiment is performed. For the sake of clarity, I’m gonna show a representation of a double stranded library fragment: XXXXX-5’ACTGC———————–TTTTTT3′-OOOOO XXXXX-3’TGACG———————–AAAAAA5′-OOOOO My question is: When you load the single stranded DNA samples onto the flow…

Quality filtering prior to pseudoalignment 0 Hi, I have often read (and anecdotally confirmed) that adapter removal, quality trimming and such are not necessary for simple estimation of transcript relative abundance in a pseudoalignment framework. My tool of choice is Kallisto, and I am doing bulk RNAseq on a NextSeq,…

We are seeking a motivated Computational Biologist with hands on experience to join our team dedicated to advancing our Cardiometabolic Disease (CMD) portfolio. As a scientist in CMD, you will:Be part of creative and enthusiastic teams working on target identification and validation (TIDVAL) for heart failure, NASH, fibrosis, inflammation, obesity,…

Throughout evolution, plants and pathogens have engaged in an arms race, with plants developing resistance genes like nucleotide-binding site leucine-rich repeats (NLRs) to counteract pathogen effectors. Historically, eastern North America has been identified as a diversity hub for Erysiphe necator, the causative agent of grapevine powdery mildew (GPM). Consequently, most…

President’s Report It has been an honor and privilege to serve as your president this past year, and I look forward to my second year in this … 2023 In Vitro Biology Meeting Update The Society for In Vitro Biology (SIVB) is excited to announce that its annual meeting is…

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

Minimum requirements for a laptop to do rna seq analysis 1 Hii everyone… I have few years of break from my career as a bioinformatician. So to upgrade myself is much needed since I’m looking for a laptop to perform some rna seq, chip seq analysis (not bulk data analysis)…

Handling multiple fastq files per sample, per lane, per read out of the Cellranger bam to fastq workflow 0 For a set of downloaded bam files from PRJNA625920 in SRA, I used 10x Genomics’ “bam to fastq” tool but got 25 fastq files per sample per lane per read like…

DOI: 10.18129/B9.bioc.prebs     Probe region expression estimation for RNA-seq data for improved microarray comparability Bioconductor version: Release (3.5) The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA…

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