Question: differentially expression analysis using raw read counts
0
gravatar for ashkan
3.7 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 • 2.5k views
ADD COMMENTlink modified 3.7 years ago by Ron990 • written 3.7 years ago by ashkan110

Hi Ashkan,

Please have a look here and here.

~ Best

ADD REPLYlink written 3.7 years ago by Farbod3.3k

this tutorial is very useful

C: DE analysis by edgeR

ADD REPLYlink written 3.7 years ago by A3.8k
3
gravatar for WouterDeCoster
3.7 years ago by
Belgium
WouterDeCoster44k 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 3.7 years ago by WouterDeCoster44k
0
gravatar for Ron
3.7 years ago by
Ron990
United States
Ron990 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 3.7 years ago by Ron990
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