Tag: RNAseq

DESeq2 input from GDAC firehose

Hi guys, I hope you are fine. I’m not good in English so if you couldn’t understand my question, please feel free to reply. I’m a beginner of bioinformatics. I want to practice differential expressed gene (DEG) analysis in R. The RNA seq data I used was downloaded from broad…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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How to perform deconvolution with RPKM values

Hi Xuran, I tried to apply MuSiC to RNAseq bulk data with RPKM as the input. According to your paper(Discussion), “MuSiC can utilize RPKM if estimates of cell type-specific total RNA abundance can be provided.” I am wondering how I can incorporate cell-type-specific total RNA abundance into your function? Or…

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Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression?

Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression? 1 I’ve had some difficulties implementing this in pipelines because it randomly fails sometimes. Are there any other programs that can be used in its stead? fastq genomics rnaseq • 201 views • link updated 7 hours ago by GenoMax…

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How to label columns in HTSeq output

How to label columns in HTSeq output 0 I’ve been working to process RNAseq data and I’ve used hisat2 to align my reads to the reference genome. When I take those output files and put them into HTSeq-count using the below code, I get a count matrix but the columns…

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Bioconductor – RiboCrypt

DOI: 10.18129/B9.bioc.RiboCrypt     Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….

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python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

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RNAseq using galaxy

RNAseq using galaxy 0 @e3a40d42 Last seen 1 hour ago United States I am new to rnaseq, I am using RNA star to map the genes and count reads per gene. After running the feature counts on RNA Star output, I will like to proceed to the deseq2 for differential…

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Establishment and Characterization of FusionRed Stable Transfected Canine Prostate Adenocarcinoma and Transitional Cell Carcinoma Cells

This article was originally published here In Vivo. 2022 Jan-Feb;36(1):170-179. doi: 10.21873/invivo.12688. ABSTRACT BACKGROUND/AIM: Cancer cell inoculation is routinely used to evaluate novel therapeutic approaches in vivo. However, without reporter genes enabling deep tissue imaging, study of early tumor progression and therapeutic responses is often limited. We describe the establishment…

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tranfering sam file easy and fast way

tranfering sam file easy and fast way 0 Hi everyone I was tried to align my fastq files by hisat2 but ı couldnot able done because my computer has 4gb ram and ı get error killed. So ı was perfomed process on my friend computer but now I should solve…

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genbank to GTF in galaxy

genbank to GTF in galaxy 0 Hi all, I am working on galaxy and have a genome file in genbank format. To use featurecounts for my RNAseq, I need to convert the genbank format to a GTF format because that’s the format the featurecounts tool in galaxy expects. Now, I…

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Single cell RNAseq data analysis

Github repository  02-04 February 2022  SciLifeLab Solna, Tomtebodavägen 23b, Stockholm, Sweden This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 45 hours, including the online lectures (15 hours)…

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RNASeq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus type 16 infection, including loss of epithelial barrier function.

RNASeq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus type 16 infection, including loss of epithelial barrier function. – Fingerprint — University of Edinburgh Research Explorer Sort by Weight Alphabetically Agriculture & Biology Human papillomavirus type 16 100% keratinocytes 72% Papillomaviridae 63% infection 32%…

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Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage?

Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage? 1 I am using a SLURM HPC to run jobs and have ran into issues with storage. I have 3TB storage, and want to run over 1000 publicly available RNAseq data through my pipeline, which includes…

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featureCounts output has letters and +/- sign

featureCounts output has letters and +/- sign 1 Hello, I have created a featureCounts table and 10 of my files had weird outputs. Some values were my organism name and others were a “+” or “-“. I could not find anything about this in the manual. I tried to re-run…

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NIH-SOAR-NCI-Bioinformatics Scientist in Rockville, MD

Axle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations around the globe. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

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New bioinformatics method to analyze viral sgRNA

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

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samtools sorts allocate memory for bam_mem issues

samtools sorts allocate memory for bam_mem issues 1 Hello everyone ı am trying to convert sam to bam samtools sort -@ 8 -o UHR_Rep1.bam UHR_Rep1.sam and ı got this error samtools sort: couldn’t allocate memory for bam_mem ı check my disk memory and ı see have enough space in my…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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Integrating Bulk RNA-seq data with Single cell RNA seq data

Integrating Bulk RNA-seq data with Single cell RNA seq data 0 Hello all, recently, I had been trying to integrate bulk RNAseq data into single-cell data where I treat each sample in my bulk RNAseq data as a single cell and integrate it into the single-cell data based on the…

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Unlog transformed data in DESeq2

Unlog transformed data in DESeq2 1 @mohammedtoufiq91-17679 Last seen 13 hours ago Qatar Hi, I am using DESeq2 for analyzing Illumina RNASeq datasets. I follow the below steps; Derived raw counts (from featureCounts) > Imported counts to DESeq2 Normalised the counts via an estimation of size factors (counts(dds, normalized =…

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RPKUM

RPKUM 1 What is “RPKUM” in RNAseq analysis context? There is no description about it in the paper and I cannot find any web pages which explain about it. It could be Reads Per Kilobase of “Unit” per Million mapped reads, I guess, but not sure. RNAseq • 216 views…

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DESeq2 comparisons using contrast

DESeq2 comparisons using contrast 0 Hi all, I recently started analyzing some bacterial RNAseq data. So, I have 4 different strains and for each strain I have 2 conditions. Let’s say strains are A, B, C and D while conditions are X and Y. I have a total of 24…

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Experimental and Meta-Analytic Validation of RNA Sequencing Signatures for Predicting Status of Microsatellite Instability

doi: 10.3389/fmolb.2021.737821. eCollection 2021. Affiliations Expand Affiliations 1 Laboratory For Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia. 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia. 3 OmicsWay Corp., Walnut, CA, United States. 4 Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia. 5…

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Novo Nordisk hiring Scientist I – Bioinformatics in Seattle, Washington, United States

About The DepartmentAt Novo Nordisk Research Center Seattle, Inc. (NNRCSI) our scientists apply cutting-edge technologies to early R&D projects with the goal of bringing real change to People with Diabetes and Obesity. Your skills, dedication and ambition will help change lives for the better and you will work with extraordinary…

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Find right adapter sequence for trimming

Find right adapter sequence for trimming 0 Hello everyone I am newly start to working RNAseq analysis. I am trying to clean single end reads data according to fastqc result. It was resulted like in example as SRR309133 I was tried Illumina Adapter Sequences find it there.But after trimming result…

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Indexing with STAR

Indexing with STAR 0 Hello, I am working with RNA seq data and creating an index of reference genome Gossypium hirsutum by using STAR. STAR asks GTF annotation format while my file is GFF3. According to literature, in order to run GFF file I need to remove –sjdbOverhang 50 and…

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Adding numbers and characters to legend key in ggplot2 of UMAP clusters

Adding numbers and characters to legend key in ggplot2 of UMAP clusters 0 Hi everyone, I have a UMAP cluster, however there are so many clusters that the descriptions look clunky if i put them on the umap…but then there are too many colors if it just colors. So, i…

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Using STAR SJ.out.tab file to identify novel ncRNAs

Using STAR SJ.out.tab file to identify novel ncRNAs 0 Hi All, I am attempting to identify novel ncRNAs from a circadian RNAseq dataset. Specifically I have a ribo-depleted RNAseq timecourse with 31 samples (sample every 2 hours for 60hrs). I have run STAR (code below). I am trying to follow…

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Scientist, Bioinformatics – Leonia | Mendeley Careers

We’re hiring Bioinformatics Scientists with strong backgrounds in database development, management and analysis as they relate to human health and disease biomarkers, with the goal of improving disease prediction and prevention. With ICR, you’ll get to: Design, build, test and refine multiple large biomarker databases in collaboration with multiple ICR…

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get rRNA FASTA file for a particular bacteria

get rRNA FASTA file for a particular bacteria 0 Hey all, I was trying to find a way to get all rRNA (5S, 16S and 23S) FASTA sequences for a particular bacteria (B. thetaiotaomicron VPI-5482, which is the type strain). I wanted this file so that I could use something…

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Director of Bioinformatics Research Job Opening in Hudson, FL at M2GEN

Director of Bioinformatics Research Location:  Remote Status:  Full-time ExemptReports to:  VP Bioinformatics & BiostatisticsDirect Reports:  Build and lead a team consisting of bioinformatics research scientists that support internal business development client engagements, as well as, external academic partner research projects and biopharma sponsored bioinformatics services Who we are M2GEN is…

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Running SortMeRNA on Multiple Files

Running SortMeRNA on Multiple Files 0 Hi all, I am VERY new to SortMeRNA (I’m a PhD student taking a bioinformatics class that has been very poorly taught). I have 27 paired samples for a total of 54 samples named like this: SRR13711719_1_val_1.fq SRR13711719_2_val_2.fq. So the format is _1_val_1.fq and…

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Design formula in DESeq2

Hello, I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals treated with a chemical and my animal model is a colorectal cancer model. My variables are gender (male or female), treatment (treated…

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Lee Placito Fellowship in Bioinformatics

Job Details Lee Placito Fellowship in Bioinformatics Nuffield Department of Surgical Sciences, Old Road Campus Research Building, Headington, Oxford Grade 7: £33,309 – £40,927 per annum Contract type: Fixed term for 3 years Hours: Full-time About the role We are looking for an enthusiastic bioinformatician who has an interest in…

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Assigning Object to Function Rather than vice-versa?

R Syntax Clarification in DeSeq2 Vignette: Assigning Object to Function Rather than vice-versa? 1 Hi, I have a question about some of the R syntax present in the DeSeq2 vignette. The following comes directly from the section regarding the removal of batch effects: mat <- assay(vsd) mm <- model.matrix(~condition, colData(vsd))…

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Combining Microarray and RNA-Seq datasets visualization and comparison

Combining Microarray and RNA-Seq datasets visualization and comparison 0 Hi, I am working with some public transcriptomics datasets (both Microarray and RNA-Seq) to study gene signatures of bacterial “Infected” samples vs. Healthy Control samples. The starting point of analysis of Microarray data is .CEL files for Affymetrix (normalize using GCRMA)…

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Create junctions from Bed file for IGV visualization

Create junctions from Bed file for IGV visualization 0 Any advice for creating junctions file from a bed-like file? My bed file looks like this: chr start end chr star end I have tried to copy the format used in TopHat (junctions file). But I can’t see the junctions in…

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How to call variant by –max-depth for RNAseq

Hi everyone! I have a query regarding variant calling from a high coverage site on the basis of the maximum likelihood variant. I have RNA-seq data mapped bam file. I called variant using the below command. “bcftools mpileup –max-depth 10000 -Oz -f ref.fa sample.bam | bcftools call -mv -Oz -o…

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Easy differential expression heatmap?

Easy differential expression heatmap? 0 I’m finally getting back to an RNAseq differential expression dataset I analyzed years ago and cannot remember what tool I used to generate these simple heat maps that I really like. I think it was an online interface where I could add/take away genes from…

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GeneLab For High School Students (GL4HS) Program Is Expanding Into U.S. Schools

The GL4HS program is a 4-week intensive summer program hosted by NASA Ames Research Center and funded by NASA’s Space Biology program. 2021 was the 5th year of the popular program developed and taught by Dr. Elizabeth Blaber (Rensselaer Polytechnic Institute). Both high school students (15) and teachers (3) participate…

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Bayesian Statistical Methods for High-dimensional Multi-omics

The Biostatistics and Bioinformatics Branch (BBB) within the Division of Intramural Population Health Research (DIPHR) at the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health is soliciting applications from post-doctoral level scientists interested in the development and application of Bayesian statistical methods…

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Enrichment analysis in Pseudomonas

Enrichment analysis in Pseudomonas 0 I am doing downstream analysis of RNAseq of Pseudomonas putida. I would like to run a functional enrichment analysis, so my question: What is the best way to get the GO and KEGG annotation of Pseudomonas putida? Any recommendation will be appreciated. Thank you enrichment…

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featureCounts difference assigned reads summary file and summed up reads in feature count matrix

featureCounts difference assigned reads summary file and summed up reads in feature count matrix 0 Dear all, this might be a naive question but my googlefoo fails me. I count reads from a bam, aligend by Star against a custom hg19 genome, after running picard markDuplicates, then counting reads assigned…

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Postdoctoral Researcher in Plant-Thrips-Virus Interactions

Category Research / Academic Location Amsterdam Are you a skilled researcher in Plant Biology and intrigued by how thrips manipulates plant defenses and how microsporidia and plant viruses manipulate thrips? We are seeking a postdoctoral researcher for an ambitious project on the effectorome of thrips and the in planta interactome….

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Custom Bioinformatics pipeline validation – general guidance

Custom Bioinformatics pipeline validation – general guidance 0 Hi, I was looking how to validate custom pipelines and bioinformatics workflow (DNAseq, RNAseq, metagenomics, viral metagenomics data). I found several papers in Pubmed, specific and general, but I was wondering if there is any UK documentation about custom bioinformatics pipeline validation….

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SeqMonk rRNA from QCplot 100%

SeqMonk rRNA from QCplot 100% 1 Dear all, I have single-end RNAseq data that I mapped with Hisat2 and am looking at in SeqMonk. I plotted the QC plot (default) + Measure rRNA. I got 100 % rRNA. Which I think is impossible right? Or did I do something horribly…

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Bioconductor – DEGseq

Identify Differentially Expressed Genes from RNA-seq data Bioconductor version: 2.5 DEGseq is an R package to identify differentially expressed genes from RNA-Seq data. Author: Likun Wang <wanglikun at tsinghua.edu.cn> and Xi Wang <wang-xi05 at mails.tsinghua.edu.cn>. Maintainer: Likun Wang <wanglikun at tsinghua.edu.cn> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”)…

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Bioconductor – airpart

DOI: 10.18129/B9.bioc.airpart     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see airpart. Differential cell-type-specific allelic imbalance Bioconductor version: 3.13 Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of…

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Isolate contrasts using DESeq2 when use a combination of categorical and continuous variables

Dear community members, I am currently using DESeq2 to analyze RNASeq data from plant roots that were colonized by a fungus. But I am facing some problems regarding contrast with a continuous variable. If you have any suggestions or comments it would be great if you can let me know….

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Peripheral blood RNAseq links neutrophilic inflammation to clinical glioma metastasis | BMC Medicine

The paper presented by Zhang et al. [6] provides a more sensitive CTC measurement than the conventional CellSearch method. Their method, which is based on human telomerase reverse transcriptase (hTERT) detection, revealed new mechanisms between CTCs and innate immunity, especially pathways of neutrophil activation and neutrophil extracellular traps in gliomas….

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Peripheral blood RNAseq links neutrophilic inflammation to clinical glioma metastasis

%PDF-1.3 % 1 0 obj > endobj 2 0 obj >stream Gliomas,Circulating tumor cells,Neutrophils,Neutrophil extracellular traps Acrobat Distiller 10.0.0 (Windows); modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) application/pdf 10.1186/s12916-021-02174-3 BMC Medicine BMC Medicine, 2021, doi:10.1186/s12916-021-02174-3 Gliomas Circulating tumor cells Neutrophils Neutrophil extracellular traps Peripheral blood RNAseq…

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need some help on how to use DESeq2 for TCGA data

need some help on how to use DESeq2 for TCGA data 0 Hello, I am sorry for this newbie question, but I spent all morning trying to find it out but can’t find a clear answer anywhere. I want to normalise RNA seq data from TCGA using DESeq2. I use…

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New bioinformatics method for viral sgRNA analysis

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

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scaffold vs chromosome level assembly

scaffold vs chromosome level assembly 1 Hello all. I have two genomes from related species. One is assembled to scaffold level and the other is reported on ncbi to be assembled to chromosome level. Is it safe to report in an article the chromosome level assembly genome is more superior…

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Bioconductor – edgeR

DOI: 10.18129/B9.bioc.edgeR     Empirical Analysis of Digital Gene Expression Data in R Bioconductor version: Release (3.5) Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood…

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Empty log files from kallisto

Empty log files from kallisto 0 Hi all, I am trying to run Kallisto for my RNAseq data. The Kallisto runs smoothly but generates empty log files (0 kb). Because of that I cannot run MultiQC as MultiQC says: multiqc | Search path : C:UsersXXXDesktopSeq Raw DataXX | searching |…

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Data science intern Bioinformatics – Basel

Data science intern Bioinformatics Job ID 330038BR Oct 18, 2021 Switzerland Job Description 250! The number of genomics research projects that are waiting for your data analysis expertise every year. Your work will be important towards faster discovery and development of next generation breakthrough therapies for unmet medical need. The…

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How does “bedtools intersect -s” work with paired-end sequences?

How does “bedtools intersect -s” work with paired-end sequences? 1 Hi, I have paired-end lectures from RNAseq experiments and I want to use bedtools intersect with the force “strandedness” parameter (-s). Will bedtools take into account the paired-end reads and treat them as a single event, or will get two…

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Bioinformatics opening at VC-backed Cambridge, USA Bio-IT Startup

The role: As part of the bioinformatics team, you’ll lead the development and prototyping of our flagship bioinformatics workflows (such as: RNAseq (single-cell, bulk, spatial), ChIP-Seq, ATAC-seq (single-cell and bulk), proteomics, etc.). For a given pipeline, you’ll research available analysis methods, compare and contrast existing bioinformatics tooling options, and define…

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Comment: What is GenotypeGVCFs?

the second article is about RNASeq.. > in which cases should i use one or another? > > “However, that scaled very poorly with the number of samples, posing unacceptable limits on the size of the study cohorts that could be analyzed in that way. In addition, it was not…

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What is GenotypeGVCFs?

Hello! This article gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- says i should use HaplotypeCaller in GVCF mode and GenotypeGVCFs then, and this article gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels- advises to use HaplotypeCaller without GenotypeGVCFs. I tried the former (with one sample), and the result is similar to the result of HaplotypeCaller in non-GVCF mode, however it differs in some…

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Dice hiring Bioinformatics Analyst in Mettawa, Illinois, United States

Dice is the leading career destination for tech experts at every stage of their careers. Our client, Experis, is seeking the following. Apply via Dice today! Experis, a ManpowerGroup company has an exciting contract opportunity for a Bioinformatics analyst. This position is a 4+ months contract for one of our…

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Alignment of de novo assembled transcripts to reference transcriptome?

Alignment of de novo assembled transcripts to reference transcriptome? 0 Hi all, I started with 40 samples of raw (but trimmed) RNASeq samples. I used these as inputs for SPAdes-rna and Trinity, to assemble them without a reference. I now have 80 assembled transcriptomes (?), and I tried to follow…

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Fetch RNA seq count data for ~5 genes with mutation status of KRAS

Fetch RNA seq count data for ~5 genes with mutation status of KRAS 0 Hi everyone, I am not very familiar with the topic of RNAseq databases, but I need the following data for one specific question: I wonder about the effect of KRAS mutation on the expression of several…

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Trouble with WGCNA gene dendrogram

Trouble with WGCNA gene dendrogram 0 I am trying to plot my gene dendrogram while following the online tutorials for WGCNA. When using the function “table(bwnet$colors)” it shows that there should be 24 modules for my data. When I continue running the code for plotting the dendrogram (code below) I…

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De novo assembly of mRNA-seq has many transcripts binding to introns or genome parts (not protein coding genes)

Hi all, For the first time, I am working on some de novo mRNAseq data already analyzed by a company (the same that perfomed the sequencing). The samples are from a species for which we don’t have an annotated genome. They assembled the transcriptome with trinity (which resulted in more…

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Bioinformatics Analyst II – Bethesda

PROGRAM DESCRIPTION The Advanced Biomedical Computing Center (ABCC) is a part of the Biomedical Informatics and Data Science (BIDS) Program at Leidos Biomedical Research, Inc. The ABCC provides technology development, scientific consultation, collaboration and training, and high-performance computing support to the NCI and NIH scientists and staff. KEY ROLES/RESPONSIBILITIES The…

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UCL-BLIC/rnaseq – Giters

Introduction UCL-BLIC/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data, modified to add kallisto. The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads (STAR or HiSAT2), generates gene counts (featureCounts, StringTie) as well as kallisto abundance files, and performs extensive quality-control on the…

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Bioinformatics – Antibody discovery job with Michael Page UK

A competitive salary plus benefitsAn exciting time to join the company as they are expanding into the UKAbout Our Client Client overview My Client is a global clinical-stage biotechnology company developing novel vaccines and biologic therapeutics to treat the world’s most life-threatening diseases. They are utilising cutting-edge technology for the…

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Bioconductor – SSPA

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see SSPA. General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data Bioconductor version: 3.0 General Sample size and power analysis for microarray and next-generation sequencing data. Author: Maarten van Iterson Maintainer:…

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RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model

Background: Despite proven therapeutic effects in inflammatory conditions, the specific mechanisms of phytochemical therapies are not well understood. The transcriptome effects of Traumeel (Tr14), a multicomponent natural product, and diclofenac, a non-selective cyclooxygenase (COX) inhibitor, were compared in a mouse cutaneous wound healing model to identify both known and novel…

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Bioconductor – epistack (development version)

DOI: 10.18129/B9.bioc.epistack     This is the development version of epistack; for the stable release version, see epistack. Heatmaps of Stack Profiles from Epigenetic Signals Bioconductor version: Development (3.15) The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq,…

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Comparing RPKM (calculated from raw counts rnaseq file) between a few genes across 2 experimental conditions with a t-test : bioinformatics

Hello everyone! Very new to analyzing RNAseq data and trying to learn the process behind it. This is completely not my area, but I would like to learn and was hoping someone could give me an explanation to my question. Thank you! I’d like to know if a few genes…

Continue Reading Comparing RPKM (calculated from raw counts rnaseq file) between a few genes across 2 experimental conditions with a t-test : bioinformatics

How to define open or close gene in ATAC-seq?

How to define open or close gene in ATAC-seq? 0 May I ask how do you use your ATAC-seq data for post-alignment analysis? Here’s what I’m doing and I have a few problems: For example, there are two groups of samples, WT and KO. In order to define the peak…

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bioinformatics-core-shared-training/Bulk_RNASeq_Course_Nov21: repo for Nov 2021 course

GitHub – bioinformatics-core-shared-training/Bulk_RNASeq_Course_Nov21: repo for Nov 2021 course You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source link

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An RNAseq Analysis of Protective/Repair Pathways.CSV

Mesenchymal stromal cells (MSCs) are an adult derived stem cell-like population that has been shown to mediate repair in a wide range of degenerative disorders. The protective effects of MSCs are mainly mediated by the release of growth factors and cytokines thereby modulating the diseased environment and the immune system….

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ajwang3/WangHydrogel-RNASeq: RNA-Sequencing Pipeline for Analysis of In Vitro Liver Inflammatory Stimuli

GitHub – ajwang3/WangHydrogel-RNASeq: RNA-Sequencing Pipeline for Analysis of In Vitro Liver Inflammatory Stimuli You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here:…

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Senior Data Scientist (Machine Learning) – Job Offer at Lonza AG

Senior Data Scientist (Machine Learning) Switzerland, BaselUnited Kingdom, Cambridge Today, Lonza is a global leader in life sciences operating across three continents. While we work in science, there’s no magic formula to how we do it. Our greatest scientific solution is talented people working together, devising ideas that help businesses…

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Entrez Gene ID

Dear Seniors and all members, Me again!! I hope you do not mind me as a junior in RNAseq and tried to learn and finish my degree. Sorry for another question. I have done WGCNA and was able to identify the module associated with traits and exported data for Gene…

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how to find the expression of an inserted genes?

how to find the expression of an inserted genes? 0 Hi, everyone, I just have one question want to know how to find out the expression of an inserted genes, for example, you have a transgenic mice with human genes inserted. you know the sequence of the human genes, and…

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Transcriptomic analysis of physiological systems

Chapter contents Book contents doi.org/10.1016/B978-0-12-819770-7.00006-2Get rights and content Abstract Sequencing of the genomes for numerous avian species has ushered in the era of functional genomics or transcriptomics for both wild and domestic species. Tools for genome-wide analysis of mRNA levels in individual samples have allowed investigators to address questions related…

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FeatureCount summary in RNA_Seq analysis

FeatureCount summary in RNA_Seq analysis 0 Hi, I have a doubt about the number of reads mapped to genes in the featureCounts report. Is it possible that the number of reads mapped to genes is greater than the total number of reads? For exemple : Mapping repport : using STAR…

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Scanpy vs DeSeq for single cell RNASeq DE gene analysis

Scanpy vs DeSeq for single cell RNASeq DE gene analysis 1 What are the advantages of either in this situation? Scanpy says it is for single cell DE analysis but if I am understandign correctly single cell RNASeq is just the same as any other normal bulk RNASeq but either…

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Using normalised counts for pairwise gene correlation (pearson) across samples

Using normalised counts for pairwise gene correlation (pearson) across samples 0 Hi, I have carried out gene pairwise correlations between every pair of genes in my RNAseq data. I have done this with non-log transformed normalised counts generated from estimatesizefactors in DESeq2, as well as with VST counts and log2…

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PMD Uncovers Widespread Cell-State Erasure by scRNAseq Batch Correction Methods

Abstract Single cell RNAseq (scRNAseq) batches range from technical replicates to multi-tissue atlases, thus requiring robust batch correction methods that operate effectively across this similarity spectrum. Currently, no metrics allow for full benchmarking across this spectrum, resulting in benchmarks that quantify removal of batch effects without quantifying preservation of real…

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Filtering Gene by mean expression

Filtering Gene by mean expression 0 Dear All, Sorry for another post. I have RNAseq data and used DESeq2 pipeline for differntially expressed genes. Now I am doing WGCNA and the author suggest to filter genes based on mean expression rather than variance. I am wondering whether anyone has ever…

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Postdoctoral Fellow (Single Cell RNAseq and Gene Regulatory Networks), Julie Law Lab job with Salk Institute for Biological Studies

Description We are currently seeking a highly motivated and independent postdoctoral fellow interested in studying the spatial and temporal regulation of root genes using single-cell genomics and other high throughput phenotyping techniques. The ideal candidate will be a plant biologist who has experience in next generation sequencing techniques, root phenotyping,…

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Quantifying alternative polyadenylation in RNAseq data with LABRAT

doi.org/10.1016/bs.mie.2021.03.018Get rights and content Abstract Alternative polyadenylation (APA) generates transcript isoforms that differ in their 3′ UTR content and may therefore be subject to different regulatory fates. Although the existence of APA has been known for decades, quantification of APA isoforms from high-throughput RNA sequencing data has been difficult. To…

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Elastic Net for RNAseq data

Elastic Net for RNAseq data 1 @1c386ab3 Last seen 1 hour ago Canada I have RNAseq results from NovaSeq and after doing some differential gene expression with DESeq2, I will like to explore the Elastic Net model to select features that differentiate my two conditions. However, I haven’t been able…

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Postdoc position in Bioinformatics – Comparative Genomics

Description Posted Date 18 Nov 2021 Locations Leuven Center VIB KU Leuven Center for Microbiology Type Post doctoral Positions 1 About the Lab The lab for Systems Biology of Kevin Verstrepen is a research team at VIB & University of Leuven. Our team focuses on genomics, genetics, epigenetics, transcriptomic, and…

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What is the best way to make mapping of RNA virus from transcriptomic data?

What is the best way to make mapping of RNA virus from transcriptomic data? 0 I am mapping an RNA virus using transcriptomic data. However, when I mapped the reads with BWA I got some reads in the final bam output, otherwise, when I mapped employing TopHat the bam output…

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Deseq2 model matrix error

Deseq2 model matrix error 1 I have trying to do Deseq2 analysis for mainly mutants vs controls. I have two covariates influencing the dataset – Gender and Genotype. This is how my sample annotation file looks – sample condition genotype gender SK01 mutant hr F SK02 mutant hr F SK03…

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How to define the gene length for RPKM calculation

How to define the gene length for RPKM calculation 4 Hi guys, I would like to calculate the RPKM of my RNA seq experiment. To do this, as from the formula, I need to know the gene length. My starting point are the row reads (single end) counts resulting from:…

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Differential gene expression analysis on microarray dataset with files from two chips

Hello all, I’m used to analyzing mostly RNAseq data, microarray is a bit new to me. I’m trying to analyze data from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47183 in R. When I try to read in the .CEL files using read.celfiles() from the oligo package, it informs me that the CEL files are not of…

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Calculating gene expression dominance coefficient via DESeq2

I am interested in calculating dominance coefficients of gene expression. For this we have RNAseq data consisting of two homozygous lines (i.e. Genotype AA and BB, respectively) and of the heterozygous crosses between them (i.e. Genotype AB and BA, respectively). We have data for both sexes in each group and…

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Bioinformatics Scientist job with Arcus Biosciences, Inc.

Locations: Hayward, California | Remote, United States Summary Scientists at Arcus work in a highly embedded and highly collaborative model with colleagues across the organization. We seek a highly motivated Bioinformatics Scientist to work closely with translational and biology research scientists in the development of novel therapeutics and biomarkers in…

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filtering most variable genes

filtering most variable genes 1 Dear All, I am trying to filter most variable genes for my specific analysis. I have normalized count from DEseq2 attached here with row for genes and column for sample ID. I have found code chunk in Biostar with the following **data$variance= apply(data, 1, var)…

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