RPKM to FPKM conversion

Question

[kanwarjag]

I have RNAseq data as RPKM values (tumor vs normal) since data is paired end how could I convert to FPKM values.

Thanks

[GouthamAtla]

You may/should not convert RPKM to FPKM. You need to recalculate FPKM from BAM file. As suggested below, if you just divide by 2, they wont be true FPKM values as you do not knowif there are any read-pairs with only one-end mapped. And if there are many read pairs like that your FPKM value might not be true.

[kanwarjag]

Thanks for the explanation

Answer 1

[michael.ante]

In case of single end data, RPKM=FPKM (Reads per kilobase per million reads and Fragments per kilobase per million reads).

In case of paired end data, you have for every read-pair one fragment. Thus, divide the RPKM by two.

[kanwarjag]

very naive clarification should it be tumor RPKM/2 - normal RPKM/2

or it should be tumor RPKM-normal RPKM = X/2

[michael.ante]

If you are looking at the ratios/fold-changes, it doesn't matter. The factor 2 is cancelled:

4:1 == 2:0.5

[kanwarjag]

Got it