RNA seq differential expression analysis

Question

[rrehimi]

Dear All,

I would like to perform differential expression analysis using RNA seq fastq files (treated vs control). I am new in using Galaxy. Recently I performed the analysis following youtube tutorial, using limma-Voom and I already have list of significant genes. Now I just came to know that I should normalize my RNA seq data.

My question is

• How can I normalize my RNA seq data before analysis or after?
• How can I get FPKM counts for my data?

Thank you in advance,
Rizwan

[seta]

You should provide row count (without normalization) for doing DEG analysis by relevant tools such as, edgeR or DEseq.

[rrehimi]

Thanks! Could you please explain the DEseq2 method using Galaxy step by step? Input files?

[swbarnes2]

No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.

[BioinfGuru]

https://help.galaxyproject.org/

Answer 1

[Mohamed Abderrahmane]

The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.