Tag: RNAseq

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Failed to open error: RNAseq Analysis 1 I am getting an error message saying that the files failed to open but it is only the second read for each file not the first read. They are in the same directory as the first read so I am not sure why…

DOI: 10.18129/B9.bioc.dreamlet   Cohort-scale differential expression analysis of single cell data using linear (mixed) models Bioconductor version: Release (3.18) Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of…

DOI: 10.18129/B9.bioc.CountClust     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CountClust. Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models Bioconductor version: 3.10 Fits grade of membership models (GoM, also known as admixture models) to cluster RNA-seq gene expression…

how to count the number of reads align per viruses in my sample 3 Hello, I would like to count the number of reads aligning per viruses in my sample based on the output of minimap2 in a bam file. Does anyone how to proceed? By using the command: samtools…

DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment 0 Hello, I have RNAseq coming from CDX models that were treated with DMSO and another compound (condition). I have 12 CDX models in total, 6 were implanted with cell1 (4 DMSO, 2 treated) and 6 with cell2 (3DMSO, 3 treated). I would…

STAR GeneCounts for most genes are 0 0 Hello all, I am relatively new to this field. I am doing an RNA-seq alignment and expecting a gene count output for a prokaryote genome. I have an annotation GTF file in which I have converted the third column into “exon” for…

error uploading gct file to gsea 0 Hello everyone I’m trying to upload my gct file of the normalized RNAseq counts for mouse into GSEA. I get errors that the last line in my gt file has bad info. I have changed the number of probes in the gct file,…

Effect of Bootstrapping/Gibbs Sampling in Salmon Counts 2 Hi Everyone, I am a bit confused about the difference between Gibbs Sampling and Bootstrapping when it comes to Salmon and how these procedures affect downstream analysis. For context, I am trying to do analysis of 49 matched cancer vs. normal RNAseq…

Snap frozen Postnatal day4 murine kidney tissues were crushed using micropestles in RLT Buffer and RNA was extracted from these tissues using QiaShredders followed by Qiagen RNAeasy Mini Kits according to manufacturer’s protocol. RNA concentration and integrity were determined by Aligent bioanalyzer. cDNA library preparation was carried out using NEB…

RNAseq how to map Mouse+Virus Genome with STAR 0 I have Fasta and GTF files from the mouse and virus genome I would like to map to. From what I have read its best to combine the Fasta and GTF files but I’m not sure how this is accomplished. For…

Hi Lisa, You also need to modify the gtf annotation file using: sed ‘/^#/d’ annotation_file.gtf > annotation_file_no_header.gtf Best, Alex > On 12. Oct 2022, at 15:07, Bora Uyar <borauy…@gmail.com> wrote: > > You would need to check how your fasta headers look and how the chromosomes are represented in…

duplicates issues when trying to convert long to wide in R 1 library(dplyr) library(tibble) library(tidyr) df <- test %>% mutate(row_id = model_name) %>% pivot_wider(names_from = gene_symbol, values_from = fpkm) ### Warning message: Values from `fpkm` are not uniquely identified; output will contain list-cols. • Use `values_fn = list` to suppress…

How to proceed after Kraken2 analysis 0 Hello, I am working on tracking and tracing of viruses in plant seed lots. I have total RNAseq data from the seed lots (around 200 samples). I did a kraken2 analysis to fish out certain viruses which we are interested in. For each…

World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….

Adipose tissue is usually classified on the basis of its function as white, brown or beige (brite)1. It is an important regulator of systemic metabolism, as shown by the fact that dysfunctional adipose tissue in obesity leads to a variety of secondary metabolic complications2,3. In addition, adipose tissue functions as…

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DOI: 10.18129/B9.bioc.ClusterFoldSimilarity   This is the development version of ClusterFoldSimilarity; to use it, please install the devel version of Bioconductor. Calculate similarity of clusters from different single cell samples using foldchanges Bioconductor version: Development (3.19) This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes)…

My Bioconductor package is receiving Errors about a package not existing. I have an R package with Bioconductor. In the vignettes folder, I have several .Rmd files that have the following chunk at the top: title: ‘Manuscripts’ package: pkgName bibliography: pkgName.bib output: **BiocStyle**::html_document: toc_float: true tidy: TRUE border-width: 5px vignette:…

Is my data too noisy for DESeq? Should I model noise as unwanted variation? 0 I am trying to relate a factor (sensitivity) to gene expression. I have ~40 samples of breast cancer, each a different cell line, from a few lung cancer subtypes. When I model my known clinical…

zero counts for all genes in RNAseq data of Ferret 0 I have bulk RNAseq data from Ferret and trying to get counts per gene. to do so I used hisat2 and got the genome from here: hgdownload.soe.ucsc.edu/goldenPath/musFur1/bigZips/musFur1.2bit after aligning the fastq files I used htseq and the following command:…

DOI: 10.18129/B9.bioc.CDI   Clustering Deviation Index (CDI) Bioconductor version: Release (3.18) Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be…

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Bulk RNAseq Salmon index building which transcriptome to use 0 Hi all, I am new to the platform. I was wondering what the common/best practice is regarding building a Salmon index for bulk RNAseq analysis of human cells. The tutorial for Salmon/Alevin is using the complete transcriptome from GENCODE (gencode.vM23.transcripts.fa.gz,…

rMATs seems to have run successfully, but there are no events written to any of the output files.  read outcome totals across all BAMs USED: 359718803 NOT_PAIRED: 0 NOT_NH_1: 191473914 NOT_EXPECTED_CIGAR: 3103528 NOT_EXPECTED_READ_LENGTH: 0 NOT_EXPECTED_STRAND: 0 EXON_NOT_MATCHED_TO_ANNOTATION: 8901301 JUNCTION_NOT_MATCHED_TO_ANNOTATION: 2461094 CLIPPED: 0 total: 565658640 outcomes by BAM written to: /scr1/users/sangreea/l48-rnaseq/combined/temp-rmats-l48-ipsc/2023-11-01-17_39_18_273434_read_outcomes_by_bam.txt…

Pearson correlation for RNAseq data – input formats 0 Hi guys, I work with tiny crustaceans and did RNAseq on different species, each with 3 biological replicates (each replicate being a pool of 3 individuals). I want to check if there is a good correlation between my replicates. I trimmed…

Hello, I am encountering an issue with the “Graphics API version mismatch” error when using the DESeq2 package in RStudio on Ubuntu 22.04. The error occurs when attempting to save plots using ggplot2 (ggsave) within DESeq2 functions like plotPCA. I have thoroughly investigated this issue, including checking package versions, graphics…

Boes J, Slotved HC, Murrell KD, Eriksen L, Roepstorff A, Nansen P, et al. Alternative migration routes of Ascaris suum in the pig. J Parasitol. 2002;88:180–3. Article  CAS  PubMed  Google Scholar  Nikolaou S, Gasser RB. Prospects for exploring molecular developmental processes in Haemonchus contortus. Int J Parasitol. 2006;36:859–68. Article  CAS …

Evidence for the activation of TOR signaling in RNAseq data comes from multiple studies. Yu et al. found that inorganic sulfate activates TOR and promotes cell proliferation and growth in Arabidopsis. Zhai et al. demonstrated that glutamine activates the TOR pathway in the brown planthopper, Nilaparvata lugens, by promoting AKT…

DOI: 10.18129/B9.bioc.orthos   `orthos` is an R package for variance decomposition using conditional variational auto-encoders Bioconductor version: Release (3.18) `orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large…

RNAseq data from colonial invertebrates provides insights into their biology by profiling small RNAs and identifying their roles in development, transposon control, and gene regulatory networks. The given text does not provide information specifically about how RNAseq data from colonial invertebrates provides insights into their biology. RNAseq data from colonial…

Is trimming necessary for RNAseq? 0 I am performing quality control on some reads that have good FastQC metrics apart from duplication levels and per base sequence content. Is it necessary to trim these reads before alignment and downstream DE analysis, variant calling etc? I have read conflicting advice about…

Abstract Transcriptomic data obtained by single cell (sc) RNAseq or bulk RNAseq can be mined to understand the molecular activity of cell types. Yet, lowly expressed but functional genes may remain undetected in RNAseq experiments for technical reasons, such as insufficient read depth or gene drop out in scRNAseq assays….

Details Posted: 01-Nov-23 Location: San Jose , California Type: Full Time Salary: $145k – $155k USD Categories: Academic / Research Research Positions Years of Experience: 5 – 10 Salary Details: Please note this job description may not cover or contain a comprehensive listing of activities, duties or responsibilities that are…

How to extract specific region from multiple bam files and merge the outputs into single bam? 0 I have more than 50 bam files and wanted to extract the reads from a region from all those bam files and merge the outputs into a single bam. I’m using samtools for…

Testing the interaction term in single-cell RNAseq DEG analysis 0 I wonder if there is a way to test for the “interaction term” in Seurat. I have two categorical variables and would like to know if the interaction between these two variables is significantly different in a scRNAseq (2 x…

Small RNAseq analyses typically require high-throughput sequencing methods and computational pipelines for data processing and analysis. The number of determinations needed for small RNAseq analyses can vary depending on the specific research question and experimental design. In general, small RNA deep sequencing (sRNA-seq) produces several million reads, which are then…

mRNA production relation to gene length in RNASeq 1 Hi all, I’m trying to understand this normalization method comparison study : www.ncbi.nlm.nih.gov/pmc/articles/PMC6171491/ In Fig 2, B) it is mentioned – Within each condition, the two genes produce the same amount of mRNA (in bp) but gene 2 is four-fifth the…

DOI: 10.18129/B9.bioc.megadepth   This is the development version of megadepth; for the stable release version, see megadepth. megadepth: BigWig and BAM related utilities Bioconductor version: Development (3.19) This package provides an R interface to Megadepth by Christopher Wilks available at github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of…

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 spectrum of between-batch similarity. Commonly employed benchmarks quantify removal of batch effects and preservation of within-batch variation, the preservation of biologically meaningful differences between batches has been under-researched….

Successful candidates will be recent PhD graduates with high levels of curiosity and who are interested in making fundamental discoveries in understanding the molecular biology and developmental origins of pediatric brain tumors.Evaluates and analyzes data.Summarizes research findings and publish results in research journals. Develops and optimizes protocols for the lab…

Job Portal Bioinformatics PhD fellow or postdoctoral fellow for multi-omics investigation of cardiac disease Job Description The Cardiac Proteomics Group at Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen wishes to appoint a talented PhD fellow and/or postdoctoral fellow for a joint proteomics and transcriptomics…

doi: 10.1007/978-1-0716-3507-0_1. Laure-Emmanuelle Zaragosi  1 , Alizé Gouleau  2 , Margot Delin  2 , Kevin Lebrigand  2 , Marie-Jeanne Arguel  2 , Cedric Girard-Riboulleau  2 , Geraldine Rios  2 , Elisa Redman  2 , Magali Plaisant  2 , Rainer Waldmann  2 , Virginie Magnone  2 , Brice Marcet  2 , Pascal Barbry  2 , Gilles Ponzio  2 Affiliations Expand Affiliations 1 Université Côte…

DescriptionPOSITION SUMMARYThe Gerencser lab at the Buck Institute seeks a Postdoctoral Researcher to study mitochondrial signaling in type 2 diabetes (T2D). Dr. Akos Gerencser’s laboratory uses cell biology, advanced microscopy, and single-cell gene expression techniques to address fundamental questions about mitochondrial function in health and aging. A current emphasis is…