Tag: DGE

Limma returned only positive logFC values 0 I want to obtain the upregulated and downregulated genes using limma. However, all the DEGs returned by my code have positive LogFC and none are downregulated (negative LogFC). This observation is consistent across multiple distinct dataframes. Is there something wrong with my code?…

Anderson IC, Campbell CD, Prosser JI (2003) Diversity of fungi in organic soils under a moorland–Scots pine (Pinus sylvestris L.) gradient. Environ Microbiol 5(11):1121–1132. doi.org/10.1046/j.1462-2920.2003.00522.x Aria M, Cuccurullo C (2017) Bibliometrix: an R-tool for comprehensive science mapping analysis. J Informetr 11(4):959–975. doi.org/10.1016/j.joi.2017.08.007 CrossRef  Google Scholar  Artursson V, Jansson JK (2003)…

Mapping of bulk RNA-seq data and differential gene expression (DGE) Using the splice-aware aligner STAR, we mapped the RNA-seq reads to the H. bakeri genome assembly obtained from WormBase ParaSite (PRJEB15396). Among all the datasets, 93.26–95.62% of the reads uniquely mapped to the reference genome (Table 1), reflecting the high…

rna seq design matrix 0 Hi all, I have RNA-seq data and it is composed of one control group and two knockout groups, to simplify my samples are detailed below; Control_1 Control_2 AKT_KO_g1_1 AKT_KO_g1_2 AKT_KO_g2_1 AKT_KO_g2_2 These are my samples (in duplicates), so to compare all KO samples with controls…

A new study used a unique approach based on chromosome structure to determine that comb jellies, also known as ctenophores, were the first lineage to diverge from the animal tree of life, with sponges following as the next branch. Previously, it was unclear whether sponges or comb jellies were the…

On “wings” in volcano plots… 0 Apparent “wings” in volcano plots (for example, as seen here) are evidence for the relationship between fold change and p-value when expression is low in one condition and there are few replicates. If one wishes to remove or minimize these, that can be done…

A study by MBARI and collaborating scientists used gene linkages to establish that comb jellies, not sponges, are the most distantly related animal to all other animals, helping to clarify a fundamental question about animal evolution that dates back over 700 million years. Mapping gene linkages provides clear-cut evidence for…

Scientists have long debated whether comb jellies (left) or sponges (right) are the sister group to all other animals. A detailed comparison of the chromosomes of these and other animals to the chromosomes of three single-celled non-animal groups finally resolves the question. (Photos courtesy of MBARI) For more than a…

Ian Haydon Proteins designed with an ultra-rapid software tool called ProteinMPNN were much more likely to fold up as intended. Over the past two years, machine learning has revolutionized protein structure prediction. Now, three papers in Science describe a similar revolution in protein design. In the new papers, biologists at…

hiPSC cell culture and differentiation hiPSCs were maintained on 1:40 matrigel (Corning, #354277) coated dishes in supplemented mTeSR-1 medium (StemCell Technologies, #85850) with 500 U ml−1 penicillin and 500 mg ml−1 streptomycin (Gibco, #15140122). For the differentiation of cortical neurons the protocol described previously21 was followed with slight modifications. Briefly, hiPSC colonies were seeded…

How do you select DEGs for further validation? 1 Perhaps this a silly question, but I’m overwhelmed with the different ways to give context to results after DGE analysis (RNA sequencing in a disease vs healthy control context). Of course I know that one should establish criteria for significance and/or…

Hello! I’m needing some help from the more experienced ones! n_n’ I’m doing a transcriptome expression comparison using DESeq2 and I would like to be sure I’m using the right parameters. This doubt came after seeing that a gene increased the expression between different sampling points but was not included…

How to perform t-test to check if cancer samples (3 replicates ) are significantly different from normal samples (3 replicates) on R?)? 0 How to perform t-test to check if cancer samples (3 replicates ) are significantly different from normal samples (3 replicates) on R?)? t-test DGE R • 25…

scRNA-seq: How does cell number in clusters affect the number of DE genes? 0 Hi, I’m new to scRNA-seq and bioinformatics, and have some questions, which I presume might be rather basic but would hopefully help out others like me who are just starting out – couldn’t find any past…

DOI: 10.18129/B9.bioc.pairedGSEA   Paired DGE and DGS analysis for gene set enrichment analysis Bioconductor version: Release (3.17) pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes…

I am facing a problem on getting the DGElist from the function of readbismark2dGE(). It didn’t show any error. output of bismark2DGE only shows Hashing, counting. I am using google colab to get more system RAM. I am using R version R4.2.3 and BiocManager 3.16. if (!requireNamespace(“BiocManager”, quietly = TRUE))…

enrichKEGG function error 1 @d4a334e3 Last seen 4 hours ago Germany Hello, I was trying to check kegg enrichment analysis for my Bulk RNAseq DGE results, and I am getting this error –> No gene can be mapped…. –> Expected input gene ID:–> return NULL… could you kindly tell what…

I have a situation where I have a factoral independant variable ‘suicide’ with three levels ‘non_suicide’, suicide, and ‘unkown’. I have been setting up my analysis thus: suicide.non.undet <- as.factor(df$suicide) CauseofDeath.recode <- as.factor(df$CauseofDeath) Sex <- as.factor(df$Sex) Smoking <- as.factor(df$Smoking) Ethanol <- as.factor(df$Ethanol) svseq1 <- as.numeric(df$svseq1) design1 <- model.matrix(~ suicide +…

View all rows in R studio RNASeq 0 This is definitely a basic question, but I can’t seem to find a straight answer online. I am running DGE through R Studio and just calculated my normalization values, however, I have 12 lines of samples the the “e” command is only…

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, Pavel, and was edited by…

Up-regulation of ubiquitin 0 Hello, I have created two deletion S. pombe strains where I specifically deleted some of the mRNA decay factor genes. After doing a DGE analysis I found ubi4 gene coding for ubiquitin is the most up-regulated gene in both deletion strains. Is this a normal cellular…

RNA-seq analysis without replicates 1 We have RNA-seq data for 12 samples for 12 conditions. Unfortunately, we do not have any replicates and each sample corresponds to one condition. For differential gene expression analysis, I will need at least 3 replicates (or patients) for each condition to be able to…

Small RNAs are important functional molecules in organisms, which have three main categories: microRNA (miRNA), small interfering RNA (siRNA), and piwi-interacting RNA (piRNA). They are less than 200 nt in length and are often not translated into proteins. Small RNA generally accomplishes RNA interference (RNAi) by forming the core of…

Corset -D parameter 0 Hello everyone, My input was 633.679 transcripts (from Trinity.fasta) made from 10 samples, no groups defined. I run corset with default parameters and got 51.556 clusters. What bothered me is that multiple transcripts were assigned to the same cluster-ID so in the end I have 46.698…

My data has two variables: treatment (untreated vs treated) and exon number (control, 1 and 9), each with 3 replicates. So 18 samples total but 6 unique groups (untreated-ctrl, treated-ctrl, untreated-1, treated-1, untreated-9, treated-9). I started by coding everything into one design matrix, then making contrasts for all the comparisons…

Time change in expression vs time change in phenotype 0 Hello everyone; We have a prospective study for which at two time points (t1,t2) we collected blood samples and some quantitative traits Q. Using DESeq2, we can ask if the blood gene expression E at t1 or t2 is associated…

differential gene analysis 0 hello! i am working on differential gene expression of cell free RNA… In this process i have created the count matrix then calculated the log of count per matrix further calculated the Z_score and calculate the variance using log and created the boxplots…so these 2 boxplots…

RevGel-seq sample preparation workflow Experiments were performed with the RevGel-seq protocol, capable of analyzing 10,000 input cells per sample with the specially designed gelation device (Fig. S3). The individual steps shown in Fig. 1A, from cell-barcoded bead coupling to library preparation for sequencing, are more fully described below: Cell labeling Cells…

Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? 2 Hello everyone, I intend to analyze differential gene expression using a GEO dataset. The value is log2 normalized signal intensity. I know edgeR’s workflow involves log normalization. However, can I skip the normalization steps…

Stringtie does not work with NCBI GTF file? 1 Hi all, I wanted to rerun my DGE analysis to see if there were any differences between HTseq-count -> edgeR and StringTie-Ballgown. However, when I tried to run my stringtie command using the same BAM file, I got an error: “Error:…

differential expression analysis of tRFs 0 Hello everyone! I have a question regarding the processing pipeline of tRFs in rat samples. I have three groups control and two stressed conditions (unfortunately too little samples each group) I am interested in doing DGE analysis and I need to take into account…

Pseudo-bulk celltype comparison across conditions from multiple-sources 1 @84e617fb Last seen 6 hours ago United Kingdom Hi all, I am aiming to merge my dataset with other available online. Data will be SCTv2 normalised, and visual integration will be done by Harmony. For DGE analysis, I would like to perform…

Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects 1 @b99e3575 Last seen 4 hours ago India I have a dataset having 4 rna seq healthy tissue samples prepared with unstranded Illumina library and another dataset with 8 rna seq healthy tissue samples prepared…

Will filter cell by highly variable genes (HVG) selection marks DGE for the filtered out low variable genes in further analysis? 1 I want to compare DGE between treated group and control group of single-cell Seq experiment. The genes of my interest are considered to be house keeping genes. In…

Differential expression vs tissue specific expression 1 I came across an article benchmarking different tissue-specific gene expression identifying methods. I am wondering why is it not a common practice to use differential expression analysis methods, like DESeq2, to identify tissue specific genes? Practically, it can be really a time-consuming task,…

Hello community, I’m relatively new to DGE/DEG analysis using RNA-Seq data, for which I’ve seen that DESeq2 is one of the go-tos for differential gene analysis. I am a bit confused about the list of genes I am obtaining and which type of normalization methods are best to use (variance…

Hello, I analyzed some data using scanpy and now I want to do some pathway analysis. I have done DE analysis between each cluster and the rest and I want to do the pathway analysis for each cluster but I have a few questions. I initially followed the instructions from…

RNAseq for DE purpose 0 Hi all, I am totally new in the bioinformatic analysis. I am working on a project that looks at DGE among different time treatments. Besides, there is no reference genome (meaning that I need a de novo assembly step). So far, after struggling and navigating…

Estimating Fold-Changes of Lowly Expressed Genes 1 @vm-21340 Last seen 6 hours ago Brazil I am doing a DGE analysis using RNAseq data to compare three conditions. I am using a standard pipeline (Create DGEList > Filter very lowly expressed genes > TMM normalize > DGE). Since there is a…

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L, Zhang F, Zhang L, Cui L, He W, Yang J, Yao X, Zhou L, Han L, Li J, Sun S, Xie X, Lai B, Su Y, Lu Y, Yang H, Huang T, Deng W, Nielsen R, Ren J,…

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…

Hello, everyone, I’m recently meeting this problem with my analysis, which i’ve done a lots of research and asked people around but their answers are quite confusing, so if I can get more opinions, that’d be terrific and thanks at advance. So I’m doing an analysis of DEGs using Deseq2…

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…

DE analysis model matrix for paired samples 1 @tkapell-14647 Last seen 2 hours ago Helmholtz Center Munich, Germany Hi, I am analyzing a NanoString dataset where the metadata look as below: The factor of interest is the “group” and both groups are found in each mouse (“mouseID”) (paired samples). I…

My data is experimental data that has been overexpressed for a specific gene. Data samples are divided into 3 groups according to the over-expression time and each group has 3 samples. (total 9 samples) I conducted DGE analysis on the control group and one case group with DESeq2. cts <-…

For Differential Gene Expression , which indexing format is better: GFF or GTF? 0 Hello, I am working on DGE and wish to create reference index for mapping. Two file formats are used for it GFF and GTF. My question is: What is the major difference between GTF and GFF?…

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

We are looking for bioinformatics help to analyze specific data sets available from GEO / NCBI using standard bioinformatics analysis pipeline We will provide the study, design and data We will ask you to create a standard bioanalytical report that will include :– Differential gene expression, clustering – Pathway enrichment/analysis–…

Single sample analysis can be done in edgeR, while it is deprecated in DNASeq2 in 2018 probably (if you can use old DESeq version then it will work in single sample also). For egdeR you just do library(edgeR) setwd() rawdata <- read.delim(“filename”, check.names=FALSE, stringsAsFactors=FALSE) ngenes <- 10000 #no. of genes…

Filter DGElist object: keep only genes expressed in sample at the same time as a particular gene of interest 0 Hello, need some help here as I’m kind of stuck with the edgeR DGElist format. I have a DGE list named x with the following dimensions: > dim(x ) [1]…

Transcripts mapping using Salmon 0 Hi all, We have recently conducted total RNA-seq (~200M reads) and mRNA-seq (~100M reads) in the same samples. Following the RNA-seq, we used Salmon selective alignment (SA) to align the reads to the Ensembl human transcriptome. This resulted in a comparable number of reads (~40M)…

DESeq2 Not full Rank – Age & Medication 0 Hi. I’ve a data matrix which looks like this: I’m trying to carrying out DGE analysis controlling for age and medication so I used the following: design(ddsMF)<-formula(~age+medication+group) ddsMF<-DESeq(ddsMF) And end up with the error, “Full model matrix is less than full…

DESeq2 1 If deseq2 is used to analyze the differentially expressed gene, what is the effect of outliers on the results of DEGs? DEGs • 54 views DESeq2 detects automatically count outliers using Cooks’s distance and removes these genes from analysis. It also automatically removes genes whose mean of normalized…

Transcriptional noise detection and Salmon TPMs 1 Hello, I’m analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1)…

Differential Gene Expression after batch correction with DESC? 0 I recently performed batch effect correction on single cell RNA-seq data with DESC. www.nature.com/articles/s41467-020-15851-3#Sec11 eleozzr.github.io/desc/ The batch corrected clustering and dimensional reduction worked well but I would like to determine differentially expressed genes between cell populations from two different batches. I…

My bioinformatics story 1 Hi all! I am new to the bioinformatics world and due to circumstances I have been given the complete responsibility to perform a human transciptomics data-analysis without bioinformatic background and for now also without supervision. This whole project feels like a big challenge, finding a puzzle…