Question: cuffdiff output table
0
gravatar for Balatheskulter
3 months ago by
Balatheskulter0 wrote:

Hello friends!

I'm new to RNA seq and DEG's. For now I have 2 questions.

  1. I have run my cuff diff and attained fpkm values, but I'm not sure whether it is right or wrong. The article that I have caused has different fpkm value, but my log2 fold change and the log2 fold change from article is matching, Is is right!. Can I proceed?

  2. How to get the function of gene in cuff diff output, where as I have only the gene name in cuff diff output.. experts please help me proceed further.

Thanks in advance.

R rna-seq next-gen assembly • 151 views
ADD COMMENTlink modified 3 days ago by Biostar ♦♦ 20 • written 3 months ago by Balatheskulter0
3

Please don't use cuffdiff. It's an antiquated tool and there are far better ones out there.

Differential gene expression packages such as DESeq2 or sleuth should be used nowadays.

As for getting the function of a gene, can't you just do a simple search of the gene name and read the literature associated with that gene?

ADD REPLYlink written 3 months ago by dsull1.2k

thank you soo much dsull, at present, I have 10k DEG's, I can't do a simple search with gene name's one by one, so is there any way to incorporate gene function after cuff diff data in the same xl sheet.

ADD REPLYlink written 3 months ago by Balatheskulter0

Oh, I see -- with gene names (e.g. Myc, Gata1, Pou5f1), you should do some sort of enrichment analysis (e.g. gene ontology analysis).

Check out https://amp.pharm.mssm.edu/Enrichr/

Enter your list of genes there. (If you download the results table, it tells you exactly which genes are associated with which functional categories.)

ADD REPLYlink written 3 months ago by dsull1.2k

Thank you dsull , let me try it out.

ADD REPLYlink written 3 months ago by Balatheskulter0
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