Tag: RNAseq

Joint scRNAseq of B and T cells

Start Current SNIC Small Storage Projects SNIC 2022/23-318 Joint scRNAseq of B and T cells SUPR uses JavaScript for certain functions. We cannot guarantee that you will be able to use the system with JavaScript disabled. Primary Classification: 10605: Immunology (medical to be 30110 and agricultural to be 40302) Allocation…

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Difference in number of DEGs from Deseq2 and limma-voom

Difference in number of DEGs from Deseq2 and limma-voom 0 Hello, I have RNA-seq data from two different treatment groups (F and NF ) at 2 different time points (T1 and T2). The mapping was done with STAR aligner and the quantification was done with FeatureCounts. I run differential expression…

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Postdoctoral position in Bioinformatics at Uppsala, Sweden, Aug 2022

The postdoctoral fellow position in Bioinformatics is available for applicants with a doctoral degree at the Department of Cell and Molecular Biology, Uppsala University, Sweden, in August 2022. General Info Position: Postdoctoral FellowNo. of Positions: 1Research Field: Bioinformatics, Computational BiologyJoining Date: ASAPContract Period: 2 YearsSalary: Subject to norms Workplace: Department…

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Best Pipeline for De novo transcriptome SC-RNAseq

Best Pipeline for De novo transcriptome SC-RNAseq 0 Hi everyone, I’m curious what the best pipeline for single cell RNA seq is if your organism of interest doesn’t have a genome. Tools such as CellRanger need a reference genome, and bustools seems to need a reference for indexing. Is the…

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Multiple disease condition vs Normal

DESeq2: Multiple disease condition vs Normal 0 Hello! I have an mRNA dataset with one cell type and 3 different conditions (Metastatic, Primary Tumor, and Solid Tissue Normal). I would like to compare the two diseased conditions with the normal. I am using the following code but getting the understated…

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what is rnaseq – Ques Answer

rnaseq CD Genomics has been providing the accurate and affordable RNA-Seq (RNA sequencing) service for decades. We combine both Illumina (short reads) and PacBio (long reads) platforms to obtain the transcriptome that allows de novo assembly or re-sequencing for bacteria, plants, animals and humans. rnaseq CD Genomics has been providing…

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Weird over-represented sequence in sn/scRNASeq fastqc

Weird over-represented sequence in sn/scRNASeq fastqc 0 Dear Fellows I have a a weird over-represented sequences in my sn/scRNASe samples founs in fastqc report as in the photo attached. I doubt that these sequences are the source of getting ambient RNA warning? Any idea how to remove them? thank you…

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can gff2 reference used in htseq-count?

Dear all We are recently working with E.coli plasmid and tried to summarize the gene counts from our RNA-Seq samples. The short reads were mapped to E.coli plasmid using tophat which generated bam files accordingly. However, we were unable to obtain a gff3 version of our target plasmid genome, the…

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Jobs on jobactive hiring Postdoctoral Bioinformatician in Single Cell and Spatial Omics Data Analysis in Adelaide, South Australia, Australia

Full-Time, 2 Year Contract Salary range $95,000 – $110,000 At the South Australian Health and Medical Research Institute (SAHMRI), we are committed to achieving innovative, ground-breaking health and medical research that fundamentally improves the quality of life for all people. The South Australian Genomics Centre (SAGC) is a multi-institutional, national…

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rna seq – R – [DESeq2] – How use TMM normalized counts (from EdgeR) in inputs for DESeq2?

I have several RNAseq samples, from different experimental conditions. After sequencing, and alignment to reference genome, I merged the raw counts to get a dataframe that looks like this: > df_merge T0 DJ21 DJ24 DJ29 DJ32 Rec2 Rec6 Rec9 G10 421 200 350 288 284 198 314 165 G1000 17208…

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What counts as a valid biological replicate in single cell RNAseq?

Forum:What counts as a valid biological replicate in single cell RNAseq? 3 I’ve run an experiment where I collected orans from 3x healthy control mice, and 3x post-injury mice – and ended up generating around 3000 individual single cells from each sample. For consistency and cost reasons, we pooled our…

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GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq

Hi all, I am new to R and Seurat, and I am following Seurat tutorials to find anchors between RNA-seq and ATAC-seq data according to: Combining the two tutorials is difficult for a cell line data set I am using for SNARE-seq Human here. I managed to run the following…

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RPKM threshold estimation – SEQanswers

Dear All, I have a doubt in the calculation of False postitive rate while checking for FPKM threshold in a RNAseq experiment. Following the method previously published (www.ploscompbiol.org/article/…l.pcbi.1000598). I am not getting desired results. I followed the method as mentioned the publication Reads were mapped to Ensembl genes (blue) and…

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Binding of the HSF-1 DNA-binding domain to multimeric C. elegans consensus HSEs is guided by cooperative interactions

The heat-shock response is represented by a small set of genes in C. elegans We initially aimed at identifying those HSE-containing promoters that are most strongly upregulated under heat-stress conditions. Given that the HSR is complex in nematodes we used data from several heat-shock studies based on microarray and RNAseq…

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Standard for aligning smallRNA to a reference human rRNA?

Standard for aligning smallRNA to a reference human rRNA? 0 Hi, I need to label some smallRNA sequences that I know are rRNA fragments. I know that for mRNA these are discarded by aligning to the human genome and filtering out multimapped reads, but I need to try to pin…

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DESeq2 and WGCNA

DESeq2 and WGCNA 0 I am currently performing an RNAseq analysis with a dataset from a GeneAtlas where I’ve identified DEGs from different comparisons. I want to now do a co-expression analysis with these comparisons and was wondering if anybody had suggestions of tutorials I could be directed to. I…

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Deseq2 Multifactor Design – Design Forum

Deseq2 multifactor design – In fact, deseq2 can analyze any possible experimental design that can be expressed with fixed effects terms (multiple factors, designs with interactions, designs with continuous variables, splines, and so on are all possible). We have searched different posts in different forums and i can’t figure out…

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Using featureCounts and downloading Rsubread

Using featureCounts and downloading Rsubread 1 @4769e097 Last seen 23 hours ago United Kingdom I am trying to perform a count per gene analysis using featureCounts in R. I have downloaded the gtf file and edited it within R to only contain the gene ID, chr, start, end, and strand,…

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

RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model | Ian Toma – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our collection of information through the use of cookies. To…

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Index of /~ckern/FAANG_Project/Pig/DeepTools

Name Last modified Size Description Parent Directory   –   H3K4me3_Liver_P348.bw 2016-06-24 10:33 60M   H3K4me3_Liver_P348_vs_Input.bw 2016-06-24 20:31 120M   H3K4me3_Liver_P350.bw 2016-06-24 10:37 78M   H3K4me3_Liver_P350_vs_Input.bw 2016-06-24 21:09 128M   H3K4me3_MultiBigwigSummary.npz 2016-06-24 13:44 17M   H3K4me3_Spleen_P348.bw 2016-06-24 10:40 67M   H3K4me3_Spleen_P348_vs_Input.bw 2016-06-24 21:50 128M   H3K4me3_Spleen_P350.bw 2016-06-24 10:43 66M  …

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GitHub – akonecny/Bulk-RNAseq-Tumor_vs_Inflamed: TBD

GitHub – akonecny/Bulk-RNAseq-Tumor_vs_Inflamed: TBD This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. 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…

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Trimming adaptors and primers for RNAseq reads

Trimming adaptors and primers for RNAseq reads 2 Hi all, I have RNA sequencing (sequenced on NextSeq 2000) reads that I know I need to cut the adaptor sequences off of and was planning to use cutadapt to do so. I have identified the adaptor sequence in my reads, but…

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Removing replicate not clustering and group with replicate Vs without -edgeR rnaseq analysis

Removing replicate not clustering and group with replicate Vs without -edgeR rnaseq analysis 0 I am working with bacteria samples – in 3 groups that include the control, Treatment A, and Treatment B. From the PCA I find that the replicates are far apart. So I have removed the treatment…

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Bioinformatics Jobs in White Waltham, England

3.3 Principal Scientist – R&D Omics and Bioinformatics Slough, Berkshire, South East England, England £35,587 – £45,000 (Glassdoor Est.) Providing oversight and executing scientific activities with elements of study design and implementation, laboratory work, scientific review, coaching of junior…… 3.6 3.3 Director, High Throughput Biologics R&D Slough, Berkshire, South East…

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HUS1 as a Potential Therapeutic Target in Urothelial Cancer

This article was originally published here J Clin Med. 2022 Apr 15;11(8):2208. doi: 10.3390/jcm11082208. ABSTRACT Platinum-based chemotherapy is the standard of care with concern to first-line systemic therapy for metastatic disease in urothelial cancer (UC). Resistance to chemotherapy despite an initial response is linked with the ability to remove platinum-based…

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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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GSEA RNASeq

GSEA RNASeq 0 Hi friends For gene set enrichment analysis (GSEA), the software from broad institute does not accept ensemble IDs, I want to do the analysis using entrez ID or hugo ID but about 2000 genes don’t have hugo ID or entrez ID. What should I do? gene enrichment…

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Can Differential Isoform expression analysis can be performed using DESeq2 package

Can Differential Isoform expression analysis can be performed using DESeq2 package 0 @03ddb485 Last seen 9 hours ago India Hello, I am want to perform differential isoform expression (DIE) analysis for RNAseq data from human. Can I use DESeq2 for this by inputting the transcript level abundance and getting differential…

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Transcriptional profiling of macrophages reveals distinct parasite stage-driven signatures during early infection by Leishmania donovani

Infection with L. donovani amastigotes or promastigotes promotes early changes in the mRNA pool of the host cell To compare the early effects of the two life stages L. donovani in the mature mRNA pool of the host cell, total cytosolic mRNA extracts from bone marrow-derived macrophage (BMDM) cultures infected…

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Validate RNAseq salmon quantification pipeline

Validate RNAseq salmon quantification pipeline 1 Hi, I’ve written a pipeline to perform quantification from RNAseq data with salmon. I’m trying to find a way to evaluate the quality of my results. I was thinking to run the pipeline on available public dataset and compare my output with another analysis….

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Sample management for enabling successful single-cell RNAseq processing

Analysis of single cells by sequencing (scRNAseq) provides insight into the impact of cellular heterogeneity on biological mechanisms and proper sample management is a critical aspect of large-scale clinical research studies, directly influencing downstream sample quality and the subsequent ability to interrogate specific cell populations of interest. Download this poster…

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ZC2 RNAseq | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.6412442 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg)](https://doi.org/10.5281/zenodo.6412442) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg :target: doi.org/10.5281/zenodo.6412442 HTML <a href=”https://doi.org/10.5281/zenodo.6412442″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg Target URL doi.org/10.5281/zenodo.6412442 Read more here: Source link

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DESeq2 on allelic reads

DESeq2 on allelic reads 1 @ea088d93 Last seen 26 minutes ago Canada Hello, Can I use DESeq2 to perform differential gene expression on allelic reads? I have allelic reads quantified for each parental allele/copy I have 2 treatments (control vs ethanol-exposed) I want to perform differential gene expression to see…

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Bioconductor – Rsubread

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…

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Multi-tissue RNAseq reveals genetic and temporal differences in acute response to viral (IHNV) infection among three selected lines of rainbow trout with varying resistance

Utilizing RNA-seq, this study compared the transcriptomic responses of three improved strains (VSel, PSel, and CSel) of rainbow trout fry during acute stages of challenge with infectious hematopoietic necrosis virus (IHNV). The VSel strain has been selected for resistance against the specific strain of IHNV used in our challenge, PSel…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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RNAseq data DEG analysis – DESeq2 normalized data

RNAseq data DEG analysis – DESeq2 normalized data 1 1) You can’t use because those data are already normalized and log-transformed. 3) RSEM expected_count is best to start off with for differential expression. Login before adding your answer. Traffic: 2089 users visited in the last hour Read more here: Source…

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Implement tests with pytest-workflow – githubhot

Pytest workflow makes it easier to maintain larger test suites and also allows to check outputs. cf. github.com/nf-core/tools/issues/605, github.com/nf-core/rnaseq/pull/546, github.com/nf-core/sarek/tree/dev/tests Testing scenarios: Run pipeline with more than one file different parameter combinations different filenames and folder structures for cellranger run subworkflows with and without index different protocols, if we manage…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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Leiden algorithm to cluster bulk RNAseq samples : bioinformatics

Hello, I am currently analyzing a publically available dataset with ~200 samples. I want to cluster the samples based on their expression to identify disease endotypes. I already tried out hclust and NMF. I know that the Leiden algorithm is often used in single cell analysis and performs quite well…

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#1008368 – pigx-rnaseq: FTBFS: configure: error: R package rmarkdown not found.

#1008368 – pigx-rnaseq: FTBFS: configure: error: R package rmarkdown not found. – Debian Bug report logs Reported by: Lucas Nussbaum <lucas@debian.org> Date: Sat, 26 Mar 2022 21:12:04 UTC Severity: serious Tags: bookworm, ftbfs, sid Found in version pigx-rnaseq/0.0.19-2 Reply or subscribe to this bug. Toggle useless messages Report forwarded to…

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Need RNAseq dataset with many samples for machine learning project

Need RNAseq dataset with many samples for machine learning project 0 I’m looking to train a machine learning model on Alzheimer’s disease transcriptome versus non-AD transcriptome. I want to train the model to differentiate between the 2 so I can then learn which genes are most important for distinguishing. I…

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htseq-count error

htseq-count error 1 Hi, htseq-count -f bam -s yes ~/htseq-trial/SRR13826419_Aligned.sortedByName.out.bam ~refgen/gencode.v39.primary_assembly.annotation.gtf > counts.txt I am trying to run htseq-count with command above but in the err file [E::idx_find_and_load] Could not retrieve index file for ‘~/htseq-trial/SRR13826419_Aligned.sortedByName.out.bam’ 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines…

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rna seq – RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias

I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters. Aim We would like to conduct SNP discovery of these samples. Objective Our ultimate goal with this genotypic data is to search for variants (both SNPs and indels)…

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RNAseq workshop (Model Species) : April4-7, 2022

News:RNAseq workshop (Model Species) : April4-7, 2022 0 Computational Biology Core at University of Connecticut is excited to announce their upcoming RNAseq workshop Virtual RNAseq (Model) Analysis workshop April4-7 !!! Open to all! Virtual, but with live instructors! For more details and to register click here Workshop: RNAseq (model) Data…

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Data Scientist II

Data Scientist II Overview Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the…

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Bioconductor – sccomp (development version)

DOI: 10.18129/B9.bioc.sccomp     This is the development version of sccomp; to use it, please install the devel version of Bioconductor. Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data Bioconductor version: Development (3.15) A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model…

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sc/sn RNASeq

sc/sn RNASeq 0 Hi Everyone I am using cellranger to align my sc/snRNAaseq reads. I use –force cells –include introns , I get this error: *High Fraction of Reads Mapped Antisense to Genes 38.9% Ideal < 10%. This can indicate use of an unsupported chemistry type (e.g. using Single Cell…

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Pathway analysis of RNAseq data using goseq package

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

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Loop through columns to generate PCA from DESeq2 data

I’d like to generate a PCA of my bulk RNAseq data, coloured by each of my variables in the DESeq2 object “vsd”. My current code looks like this (to generate a single plot): pcaData <- plotPCA(vsd, intgroup=c(“Age”, “BlastRate”), returnData=TRUE) percentVar <- round(100 * attr(pcaData, “percentVar”)) ggplot(pcaData, aes(PC1, PC2, color=Age, shape=BlastRate))…

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CEFAS22-11 Next Generation Sequencing Services Framework: | Construction Tenders

Tender Details Reference ocds-h6vhtk-031eee Common Procurement Vocabulary Technical analysis or consultancy services Procurement Method Open procedure Value £500,000 Tender Details Reference ocds-h6vhtk-031eee Common Procurement Vocabulary Technical analysis or consultancy services Procurement Method Open procedure Value £500,000 Section I: Contracting authority I.1) Name and addresses CEFAS Pakefield Road Lowestoft NR33 0HT…

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Rangam Consultants Inc. Bioinformatics Analyst

This is a 100% Remote / Work From Home role Candidates can work 40 hours per week R exp needed 2-3 yrs of exp needed even with degree Biology knowledge Statistics analysis Need to upload process data to data base Masters degree will work Fresh Phd will also work Multi-omics…

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Dublin, Ireland | Bioinformatics Research Fellow: Understanding the production of CAR-T cell therapies

Job:Dublin, Ireland | Bioinformatics Research Fellow: Understanding the production of CAR-T cell therapies 0 Cell therapy is the transfer of intact, live cells into a patient to treat or cure a disease. Cell-based immunotherapy and in particular, modified-cell immunotherapy such as CAR-T, has been delivering spectacular results for cancer patients…

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Xena TCGA TARGET TCGx RNAseq Data

Zenodo DOI Badge DOI 10.5281/zenodo.6323594 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg)](https://doi.org/10.5281/zenodo.6323594) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg :target: doi.org/10.5281/zenodo.6323594 HTML <a href=”https://doi.org/10.5281/zenodo.6323594″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg Target URL doi.org/10.5281/zenodo.6323594 Read more here: Source link

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RNA-seq workshop: from reads to differentially expressed genes Registration, Mon 28/03/2022 at 10:00 am

Expression of interest for hands on workshop: RNA-seq analysis: from reads to differentially expressed genes. Workshop dates/times (Melbourne time): March 28th and 29th 10am-1pm EOI deadline 5pm Monday 14th March Successful applicants notified: Friday 18th March Lead trainers: Jessica Chung (Melbourne Bioinformatics, The University of Melbourne) Tom Harrop (Melbourne Bioinformatics,…

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HRJOB7442 Bioinformatics Scientist 2 (Various Locations) in Nether Alderley, Macclesfield (SK10) | Almac Group (Uk) Ltd

Bioinformatics Scientist 2 Hours: 37.5 hours per week Salary: Competitive Ref No: HRJOB7442 Business Unit: Diagnostic Services Location: Craigavon or Manchester Open To: Internal and External Applicants The Company Almac Diagnostic Services is a leading stratified medicine business, specialising in biomarker-driven clinical trials. We are incredibly proud to be involved…

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Multiple correlations RNAseq data – correction for multiple testing?

Hello all, I have performed bulk RNAsequencing of tissue (e.g. kidney) from patients with a disease (e.g. diabetes), and I would like to identify genes that correlate with a continuous clinical variable (e.g. Hemoglobin A1c). I can then obtain a Rho (correlation coefficient) and a p value for each gene….

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Postdoctoral Fellow (Single Cell RNAseq and Gene Regulatory Networks), Julie Law Lab

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, and…

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Bioconductor – atena

DOI: 10.18129/B9.bioc.atena     Analysis of Transposable Elements Bioconductor version: Release (3.14) Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification…

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Bioconductor – txcutr (development version)

DOI: 10.18129/B9.bioc.txcutr     This is the development version of txcutr; for the stable release version, see txcutr. Transcriptome CUTteR Bioconductor version: Development (3.15) Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can…

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RNASeq deseq2

RNASeq deseq2 1 Hi friends I have RNASeq data fromTCGA as HT-seq format. I want to do Deseq2. some patient names are duplicated and deseq2 dose not accept them. How would I deal with the duplicated patients? deseq2 RNASeq • 229 views • link 1 day ago by Rob &utrif;…

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The Difference Between Genome Reference(scRNAseq) And Transcriptome Reference(bulk RNAseq)

I want to know the difference between Genome Reference in scRNAseq and transcriptome reference in bulk RNAseq. But I didn’t get any better answer in any other place. I know we could download genome reference from UCSC, NCBI, ENSEMBL and GENECODE for bulk RNAseq. And here are the links below:…

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gene ID RNAseq

gene ID RNAseq 0 Hi friends How can I get gene numeric ID and hugo ID by R script? what script should I use? I have this but does not give numeric ID and hugo ID. ibrary(biomaRt) library(dplyr) library(tibble) attributeNames <-c(“ensembl_gene_id”,”external_gene_name”,”HGNC_ID”, “chromosome_name”,”description”) filterValues <- rownames(res) Annotations <- getBM(attributes=attributeNames, filters =…

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Postdoctoral position in bioinformatics – focused on single-cell immune transcriptomics – Karolinska Institute – job portal

Postdoctoral position in bioinformatics – focused on single-cell immune transcriptomics Login and apply Do you want to contribute to improving human health? We are looking for an ambitious postdoctoral fellow with solid genome-wide bioinformatics and computational biology skills to join our highly accomplished team. We offer a stimulating environment in…

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Difference of results with the same input [RNAseq analysis]

Difference of results with the same input [RNAseq analysis] 0 Hello! I am trying to optimize the treatment of some RNAseq files by splitting the input reads into several files. I am comparing the results I have obtained with: the reads input as one file the split input as several…

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Bioconductor – DaMiRseq (development version)

DOI: 10.18129/B9.bioc.DaMiRseq     This is the development version of DaMiRseq; for the stable release version, see DaMiRseq. Data Mining for RNA-seq data: normalization, feature selection and classification Bioconductor version: Development (3.15) The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them…

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How to retrieve the batch corrected data frame when using Deseq in R?

How to retrieve the batch corrected data frame when using Deseq in R? 1 I have several different RNAseq dataframes that I have merged together; they are from different studies and are raw counts. I want to correct the merged dataframe for study batch effects without getting negative values (I…

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how to deal with these???

‘Negative’ and ‘Positive’ bigWig RNAseq files: how to deal with these??? 0 @bas_work-22458 Last seen 1 day ago Netherlands Hi: Before diving into analysis of (public) RNAseq data, I discovered that the data are stored in two BigWig files per sample (i.e. carrying a ‘neg’ identifier, the other a ‘pos’…

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Multi-factor paired RNAseq differential analysis with DEseq2

Hello, I’m working with an RNAseq dataset that looks at plants that are either infected with a fungus or have been left uninfected. I have both male and female genotypes, and those have been cloned, with one clone of each genotype getting inoculated while the other clone serves as the…

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r – Can I analyze RNAseq data from two different cell types using the design matrix model.matrix(~0 + group + celltype)?

I have two cell types(11C and 13C) and two groups (KO and CTRL). sample celltype group 11C-17 11C KO 11C-84 11C KO 11C-C 11C CTRL 13C-17 13C KO 13C-84 13C KO 13C-C 13C CTRL As shown in the PCA plot, the cell type is the dominant difference. But, I’d like…

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Bioinformatics Scientist Job Opening in Seattle, WA at Alpine Immune Sciences

Job Posting for Bioinformatics Scientist at Alpine Immune Sciences Alpine Immune Sciences is applying our platform discovery technology to bring innovative new therapies to people living with serious or life-threatening illnesses or conditions, such as cancer and autoimmune/inflammatory diseases. Exciting challenges lie ahead—guided by our core values, we’ll…

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UMItools dedup deduplication taking too much time + RAM

I have some RNAseq data from miRNAs that I have processed with Bowtie2 (aligning to miRBase). Now, when doing the deduplication with umi_tools dedup I find that some of the files take a lot of time+RAM to finish (some files take around 3-4 minutes and 4-5GB of RAM and some…

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Active Motif Incorporated Announces the Acquisition of Amaryllis Nucleics and their proprietary RNASeq workflow

CARLSBAD, Calif., Jan. 27, 2022 /PRNewswire/ — Active Motif Incorporated, a company with the vision of bringing epigenetics more deeply into precision medicine, announced that it has purchased Amaryllis Nucleics, a Bay Area-based start-up company focused on proprietary RNA Sequencing methods. Amaryllis Nucleics provides Active Motif with a streamlined, low-cost…

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Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs

doi: 10.1093/nar/gkac019. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA. 2 Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA. 3 Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA….

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Introduction to RNA-seq data analysis – Extended Materials

Introduction to RNA-seq data analysis – Extended Materials | cruk-summer-school-2021 Github repo for 2021 CRUK-CC Bioinformatics Summer School (tinyurl.com/crukss2021) Taught remotely Bioinformatics Training, Craik-Marshall Building, Downing Site, University of Cambridge Supplementary materials These files contain some additional information and exercises not included during the taught course. Obtaining public data Raw…

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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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