Tag: DGE

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…

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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…