GC content analysis using EdgeR

Hi!

I´m new in EdgeR. I have a table count reads from RNAseq. How can I perform a GC conten analysis using EdgeR (steps)?

Thanks!

rna-seq

• 1,160 views • link

updated 7.8 years ago by h.mon

• written 7.8 years ago by vhelizarraga •

1 answer

You can't, edgeR is a R package to perform differential gene expression analysis.

What do you mean by "GC content analysis"?

• 1 views • link

written 7.8 years ago by h.mon

More posts like this

RNA-seq with normalized cpm count
written 2.4 years ago by GiV17 •

Hi all, I have a question. I have a cpm matrix count of a rnaseq experiment obtained from metatranscriptomics analysis. How can I perform a …
Tutorial for ROC curve analysis using DE RNA data in R
written 4.4 years ago by MS •

Hi, I want to perform ROC analysis using DE RNA data in R studio. I am new so I want a tutorial that explains all …
How to get normalized count table from DESeq?
written 4.7 years ago by leranwangcs •

Hi, I'm using Deseq compare differential abundance. Here is my code: ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type) geoMeans <- apply(counts(ds.all),1,gm_mean) ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans) dds.all …
Differential gene expression analysis with RPKM
written 5.8 years ago by koaeb •

Hi, I know there are a lot of discussion about why we can't perform DE analysis (by EdgeR or DEseq )using RPKM, but this is …
gene expression RNAseq
written 6.9 years ago by domingues.pesca •

Hi all I am new in bioinformatics and need some help. I did a DEG analysis from Trinity transcripts using a *de novo* reference. First …
Stringtie: use htseq-count or prepDE.py to extract reads?
written 7.3 years ago by heyang •

Hi All, I am currently working on downstream analysis of my RNAseq data. I have been using stringtie and its prepDE.py to extract the reads …
DE analysis with two samples in multiple samples
written 9.0 years ago by Satyajeet Khare

I use `EdgeR` to perform DE analysis using the standard protocol. The steps are as follows. 1. Alignment using `HiSAT2`, 2. Count matrix generation using …
GC content for RNA-Seq data
written 9.1 years ago by sukesh1411 •

Hi I am new to the rna-seq data analysis. I have rna-seq data of leaf. I would like to perform transcriptome assembly using trinity. Before …
How to do sequencing reads technical analysis and biological quality analysis for RNASeq dataset?
written 10.9 years ago by nalandaatmi •

Hi all, I have recently started to work on RNASeq analysis. I need to do the following two aspects of analysis first, before performing the …
Draw Heatmap Or Do Pca Analysis With Raw Read Counts?
written 13.5 years ago by camelbbs

<p>Hi,</p> <p>I want to ask a question about viewing RNAseq data with raw read counts. After I get the raw reads counts from HTseq-count or …