Question: differentially expression analysis using raw read counts
0
gravatar for ashkan
2.5 years ago by
ashkan110
ashkan110 wrote:

I have raw read count from RNA-seq(meaning I aligned fastq files and got raw read counts using HTSeq). is there any way to do differentially expression analysis to identify DEGs? thanks

rna-seq • 1.9k views
ADD COMMENTlink modified 2.5 years ago by Ron920 • written 2.5 years ago by ashkan110

Hi Ashkan,

Please have a look here and here.

~ Best

ADD REPLYlink written 2.5 years ago by Farbod3.2k

this tutorial is very useful

C: DE analysis by edgeR

ADD REPLYlink written 2.5 years ago by F3.4k
3
gravatar for WouterDeCoster
2.5 years ago by
Belgium
WouterDeCoster38k wrote:

Have a look at DESeq2, edgeR, limma-voom and perhaps this workflow from Bioconductor http://www.bioconductor.org/help/workflows/rnaseqGene/

ADD COMMENTlink written 2.5 years ago by WouterDeCoster38k
0
gravatar for Ron
2.5 years ago by
Ron920
United States
Ron920 wrote:

Here is tutorial using DESEQ2

https://www.r-bloggers.com/tutorial-rna-seq-differential-expression-pathway-analysis-with-sailfish-deseq2-gage-and-pathview/

ADD COMMENTlink written 2.5 years ago by Ron920
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 789 users visited in the last hour