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RNA seq differential expression analysis

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

rna-seq normalization
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updated by BioinfGuru BioinfGuru • written by rrehimi • rrehimi

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

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written by seta seta

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

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written by rrehimi • rrehimi

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

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written by swbarnes2 swbarnes2

1 answer

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

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written by Mohamed Abderrahmane • Mohamed Abderrahmane

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