Tag: RNAseq

Research Fellow, Bioinformatics job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description We are seeking for a full-time bioinformatician in the cancer biology laboratory of Dr. Shruti Bhatt in the Department of Pharmacy at the National University of Singapore.  Check out Bhatt lab research focus, via this link:   pharmacy.nus.edu.sg/team/asst-prof-shruti-bhatt/ We are looking for candidates who share our excitement to…

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why do i get much more significant genes and wierd volcano plot with DESeq2 for my RNAseq dataand LRT not with Walds test

I’m looking into the differentially expressed genes in heat-stressed animals versus normal ones. I have a data matrix of 40 samples of different conditions and using contrast I compare each one to its the control. I want to look at the heat stressed the other 3 are non-stressed old versus…

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Assessing spermatozoal small ribonucleic acids and their relationship to blastocyst development in idiopathic infertile males

Vander, B. M. & Wyns, C. Fertility and infertility: Definition and epidemiology. Clin. Biochem. 62, (2018). Sun, H. et al. Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990–2017: Results from a global burden of disease study, 2017. Aging 11, 10952 (2019). Article …

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Higher Dimensional RNASeq Clustering Significance

Higher Dimensional RNASeq Clustering Significance 0 @73ef4518 Last seen 29 minutes ago United States Looking at the principal components of our RNASeq data, there is clear separation between the diseased and controlled, however, this separation is in the 5th principal component, which only accounts for 0.45% of variance. There is…

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featureCounts paired end reads wrongly assigned on the single end mode

featureCounts paired end reads wrongly assigned on the single end mode 0 Hello! I have RNAseq data from samples containing 2 to 3 bacterial strains each. For the analysis I performed FastQC, trimmomatic to remove adapters and then Bowtie2 to align the reads to the reference genomes. I have one…

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How to convert single-cell RNAseq filename.mtx.gz to seurat object

How to convert single-cell RNAseq filename.mtx.gz to seurat object 0 Hi All, I need your great help with my public scRNAseq data obtained from GEO dataset analysis. For example, if I want to access this dataset (GSE118019) to convert it into Seurat object? There is no separate barcode, features, matrix…

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Bioinformatics Analyst III Position In South San Francisco, CA

Job Description To discuss more about this job opportunity, please reach out to Chitrank Rastogi (LinkedIn URL – www.linkedin.com/in/chitrank-rastogi-55119a102/), email your updated resume at chitrank.rastogi@collabera.com or give me a call at (425) 523-1648. Thank you! Job Description:Job Roles & Responsibilities: The Genomic Research Center Computational Oncology group (GRC-CO) is seeking…

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Rsubread featureCounts outputs dozens of temp files, no counts

Rsubread featureCounts outputs dozens of temp files, no counts 1 @83165de1 Last seen 16 hours ago United States Hello, I am having trouble getting an output file in Rsubreads using featureCounts. I want to set up my data to run analysis of differential expresssion in EdgeR. I’m running about 40…

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Bioinformatics Programmer 3 – 119617

UCSD Layoff from Career Appointment: Apply by 10/25/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 11/3/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance. The Bioinformatics Programmer’s will apply complex bioinformatics concepts to design and…

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Expression level of mutant genes in RNAseq data

Expression level of mutant genes in RNAseq data 1 Hello, I have WES data from matched tumor and normal samples and mutants called from these data (in MAF files). From my understanding, if I sequence the tumor sample RNA, and run a routine RNAseq data analysis pipeline, the counts I…

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Is dropout a big concern (or factor) when analysing single cell RNAseq?

Is dropout a big concern (or factor) when analysing single cell RNAseq? 0 When analysing single cell RNAseq is drop-out (% dropout by count) a huge factor that needs to be paid attention? I see mixed opinions (publications, workshops, etc) on how to deal with dropouts whether to use imputation…

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Is it okay to use dna.toplevel file for alignment if primary assembly file is not available?

Is it okay to use dna.toplevel file for alignment if primary assembly file is not available? 0 I cannot fine the primary assembly file for glycine max on ensembl plants. Can I use dna.top.level file or should i just stick to the sm files? I have read somewhere that “If…

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Scientist, Discovery Bioinformatics Jobs in San Diego, CA

Scientist, Discovery Bioinformatics Jobs in San Diego, CA at Velia Title: Scientist, Discovery Bioinformatics Company: Velia Location: San Diego, CA Velia is a transformative biotech company with the ambitious goal to harness the therapeutic potential of a novel class of human peptides, also known as microproteins. Building upon our founders’…

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Bioconductor – clusterExperiment

DOI: 10.18129/B9.bioc.clusterExperiment     Compare Clusterings for Single-Cell Sequencing Bioconductor version: Release (3.5) Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets. Author: Elizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb] Maintainer: Elizabeth Purdom <epurdom at…

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Combine scRNAseq data for bulk analysis using DESeq2

Combine scRNAseq data for bulk analysis using DESeq2 0 @evocanres-17914 Last seen 2 hours ago United States I have scRNAseq data from Fluidigm C1 platform, but I have low number of cells (sample 1 ~30, sample 2 ~ 20). Can I merge the fastq files for each samples and treat…

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Low number of nCount_RNA in single-cell RNAseq clusters?

Low number of nCount_RNA in single-cell RNAseq clusters? 0 Hello, after standard Seurat workflow, I checked the metrics of each cluster in the object. Please see the attached picture. How may I explain, in some of clusters, such as cluster 9 which has low nCount_RNA and nFeature_RNA but with an…

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Whole Transcriptome Data Analysis Course, EMBL Advanced Training Centre, Heidelberg, Baden-Wurttemberg, Germany

Overview Whole Transcriptome Data Analysis Course is organized by European Molecular Biology Laboratory (EMBL) and will be held from May 21 – 26, 2023 at EMBL Advanced Training Centre, Heidelberg, Baden-Wurttemberg, Germany. Description:This course will teach biological researchers how to analyze biological data sets using open-source software. Most of the…

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Manually adding genes of interest to transcriptome for RNASeq DE?

Manually adding genes of interest to transcriptome for RNASeq DE? 1 I have been given some RNASeq reads by a collaborator and have been asked to assess whether there is differential expression between treatments in 6 genes of interest to my collaborator. Unfortunately, this is a non-model organism and so…

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Isolation of Preadipocytes from Broiler Chick Embryos

The present protocol describes a simple method for isolating preadipocytes from adipose tissue in broiler embryos. This method enables isolation with high yield, primary culture, and adipogenic differentiation of preadipocytes. Oil Red O staining and lipid/DNA stain measured the adipogenic ability of isolated cells induced with differentiation media. Primary preadipocytes…

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Postdoc Position in Bioinformatics, Neuroscience and Drug Discovery

The Laboratory for the Research of Neurodegenerative Diseases headed by prof. Bart De Strooper is a vibrant environment where key issues related to Alzheimer’s disease are tackled. We are currently looking for a highly skilled and motivated postdoc to join our multidisciplinary project on the cellular response to Alzheimer’s pathology…

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Index of /gbdb/hg38/gtex/cov

Name Last modified Size Description Parent Directory – GTEX-1C475-0726-SM-73KVL.Esophagus_Muscularis.RNAseq.bw 2019-12-16 09:16 160M GTEX-1C475-1826-SM-73KWA.Skin_Sun_Exposed_Lower_leg.RNAseq.bw 2019-12-16 09:16 194M GTEX-1GMR3-0626-SM-9WYT3.Artery_Coronary.RNAseq.bw 2019-12-16 09:16 177M GTEX-1H1E6-0826-SM-9WG83.Pancreas.RNAseq.bw 2019-12-16 09:16 122M GTEX-1HFI6-0011-R7b-SM-CM2SS.Brain_Putamen_basal_ganglia.RNAseq.bw 2019-12-16 09:16 172M GTEX-1HGF4-0011-R5b-SM-CM2ST.Brain_Caudate_basal_ganglia.RNAseq.bw 2019-12-16 09:17 178M GTEX-1HSGN-0726-SM-A9G2F.Thyroid.RNAseq.bw 2019-12-16 09:17 194M GTEX-1HSKV-0011-R1b-SM-CMKH7.Brain_Hippocampus.RNAseq.bw 2019-12-16 09:17 149M GTEX-1I1GU-1226-SM-A9SKT.Esophagus_Gastroesophageal_Junction.RNAseq.bw 2019-12-16 09:17 186M GTEX-1IDJC-1326-SM-CL53H.Colon_Transverse.RNAseq.bw 2019-12-16 09:17 217M GTEX-1IDJU-1026-SM-AHZ2U.Vagina.RNAseq.bw 2019-12-16…

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Log2FC values slightly higher in some genes after DESeq2 shrinkage

Hi, I have a question about DESeq2 LFCshrinkage: Is it possible that some genes have a slightly higher LFC after shrinkage? It happened during my RNAseq DE analysis, I have very deeply sequenced samples with large base means. I tried visualizing using MAplot check, and it looks fine. I’m mainly…

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TPM and RPKM normalization from counts dataframe

TPM and RPKM normalization from counts dataframe 2 Folks: I have two dataframes for counts information from two RNAseq data… is there a quick way to get from counts to TPM or RPKM or both efficiently? Thanks RNA-Seq • 3.5k views • link updated 5.8 years ago by Ron &starf;…

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Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma | BMC Medical Genomics

Sia D, Tovar V, Moeini A, Llovet JM. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene. 2013;32(41):4861–70. CAS  Article  Google Scholar  Sungwan P, Lert-Itthiporn W, Silsirivanit A, Klinhom-On N, Okada S, Wongkham S, Seubwai W. Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma. PeerJ. 2021;9:e11067. Article …

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between results of RNAseq and absence/presence of Type3 Secretion System

Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System 1 Dear All, I have a “How would you solve” kind of question. I have two sets of tables : 1. Log2FoldChange table and 2. Effectors Table. Firstly, the Log2FoldChange table was obtained by performing…

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Bioconductor – cqn (development version)

DOI: 10.18129/B9.bioc.cqn     This is the development version of cqn; for the stable release version, see cqn. Conditional quantile normalization Bioconductor version: Development (3.16) A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. Author: Jean (Zhijin) Wu, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen <kasperdanielhansen at…

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Senior Associate Computational Toxicologist job with Pfizer

This position will be responsible for the continued development and maintenance of RNAseq data analysis and other bioinformatics pipelines. DSRD has invested heavily in our capacity to generate genomic and transcriptomic data, including quickly evolving areas such as single cell RNAseq and spatial transcriptomics. The successful candidate will be responsible…

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Senior Bioinformatics Scientist at Roche July, 2022

Position summary As a Senior Bioinformatics Scientist, you will provide bioinformatics support for product research and development, as well as the marketing, sales and on-market product support teams. You will collaborate and innovate with bioinformatics scientists, software engineers and  molecular biologists to build products that will impact patient care for…

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Could not locate a HISAT2 index to basename

Could not locate a HISAT2 index to basename 2 First time trying out HISAT2 and I’m having a problem here, even with the pre-made indices for GRCH38. $ hisat2 -x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran -1 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R1_001.fastq.gz -2 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R2_001.fastq.gz -S tmp.sam Error follows Could not locate a HISAT2 index corresponding to basename “/share/projects/RNASeq/data/reference/GRCh38/grch38_tran” Error:…

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Batch effect correction in 2 conditions + 2 genotypes + interaction term design

Dear all, I am analyzing RNAseq data with DESeq2 for a dataset that resemble the type “2 conditions, 2 genotypes and interaction term”; specifically I have healthy donors and patients for both male and female population. I am interested in obtaining: 1- genes modulated in male patients as compared to…

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Increased GC content after trimming RNAseq data

Increased GC content after trimming RNAseq data 0 Hi, I’ve trimmed rnaseq data (PE 100bp reads) thanks to trimgalore ro remove adapters. After trimmming I’ve noticed an increased on GC content (see below), specifically for reverse reads, and for high value of GC %. I’m having trouble to understand where…

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lncRNA analysis tutorial

lncRNA analysis tutorial 2 hello, I would like to ask if there is some good tutorial concerning analysis of lncRNA along RNAseq analysis? like practical example. thank you for your help. lncRNA RNA-seq • 458 views Generally speaking, doing differential expression (DE) or transcript discovery on lncRNA is no different…

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Mapping reads using kallisto – rna seq analysis

Mapping reads using kallisto – rna seq analysis 0 Hi, I’m trying to map reads to a reference genome using kallisto for rna seq analysis with terminal on mac and the following command keeps loading for hours and won’t run. I’m not exactly sure where I’ve gone wrong. kallisto index…

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Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (0,2 and 4h) with 3 group (1 control, 2 treated)

Dear Experts, I have RNAseq data from 6 different plant samples (2 control, 2 Sensitive, and 2 tolerance), and different location of one species. I am trying to see the effect of the different groups at different time points, but after going through all the posts and vignettes I am…

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load csv file to edgeR

load csv file to edgeR 0 Hi, I have a differential gene expression file created by edgeR and i wonder how i can import this csv file back to use goana() in the edgeR package? Best, RNAseq edgeR • 40 views • link updated 2 hours ago by Ram 36k…

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Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation?

Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation? 0 I am working on RNASeq data for DE from a non-traditional organism (Artemia franciscana, a eukaryotic arthropod) whose draft genome was published last year. I should note here that although the genome was assembled with…

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Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq

Software official website : Hisat2: Manual | HISAT2 StringTie:StringTie article :Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols It is recommended to watch the nanny level tutorial : 1. RNA-seq : Hisat2+Stringtie+DESeq2 – Hengnuo Xinzhi 2. RNA-seq use hisat2、stringtie、DESeq2 analysis – Simple books Basic usage…

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PCR duplicates in FFPE RNASeq

PCR duplicates in FFPE RNASeq 0 Dear all, I am working on 100 RNASeq data generated with a stranded protocol and a Novaseq run. I need to perform variant calling on these samples, however I am facing some problem. I have not access to DNA so exome/targeted amplification is not…

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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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