cuffdiff - cummerbund - fold change

[Parharn]

Hi,
Is there a way that I can have a list of genes with expression fold change of X, instead of significant genes, using cummeRbund and cuffdiff?

Thanks,
Parham

[TiborNagy]

Yes, in the cuffdiff output folder there is a gene_exp.diff file, the 10th column is the log2 fold change.
awk -F"\t" '{if($10==X)print $1}' gene_exp.diff # where X is the specified fold change.

[Parharn]

Yes, I could see the log2 in the data file but I didn't know how to list them using command lines. I am not a linux expert. However I tried your command line but it gives this error:

> awk -F"\t" '{if($10==1.5)print $1}' gene_exp.diff #
Error: unexpected string constant in "awk -F"\t""

and could you write what if I want it to show all the genes with a fold change of equal and bigger than X? thanks.

[Parharn]

oops I guess I made a mistake. I ran the command in R then!
Now I tried it in normal terminal, I don't know what you call it. But it gave me a long list! So it seems it works. I still appreciate to know how to change it to show values equal and bigger/smaller! thanks.

Update: all the files it sorted has a characteristic like:

SPATRNATHR.02 SPATRNATHR.02 SPATRNATHR.02 I:2433047-2433119 tag5 tag7 NOTEST 0 0 0 0 1 1 no

[jeales]

If you're not familiar with R or cmd line then just import it into excel, sort by log2 fold change then remove the range of values you don't want

[Parharn]

Thanks jeales.