calculate FPKM/RPKM values by user friendly software

Question

[singh.bioinfo]

Hi,

I have RNA-seq data, different treatments and replicated samples.I would like to calculate FPKM/RPKM values, and calculate the fold-change by dividing the mean values.Does any one know the formula to calculate it manually or any user friendly software to calculate these values?

Thank you,

[singh.bioinfo]

Thanks everyone for your helpful suggestions.

Answer 1

[Benn]

Hi,

There are many posts about FPKM/RPKM, see 'similar posts' at the right side of the screen.

Conclusion is that FPKM/RPKM is not recommended for your kind of analysis. Use raw read counts and tools such as limma or edgeR or DESeq.

If you still want to use RPKM, you can use excel if that's user friendly enough.

Answer 2

[Govardhan Anande]

Hello, you can use following formula to calculate rpkm and fpkm.

 RPKM(Reads Per Kilobase per Million) = [# of mapped reads]/([length of transcript]/1000)/([total reads]/10^6)

FPKM(Fragments Per Kilobase per Million) = [# of fragments]/([length of transcript]/1000)/([total reads]/10^6)

And fold change is very simple, see here.

Answer 3

[michael.ante]

Hi,

in terms of user-friendliness, have a look at Galaxy. It is a workbench combining lots of tools for analysis of SEQ-data. You can upload your data and run for instance the TopHat-Cufflinks pipeline or Sailfish.

Cheers,

Michael